All Gene Supplementary Material - Additional samples removed.

Load Libraries

# libraries used for analysis
library(edgeR)
library(limma)
library(quadprog)
library(ruv)

# libraries required for graphics
library(ggplot2)
library(reshape2)
library(EDASeq)
library(RColorBrewer)
library(VennDiagram)
library(data.table)
library(dplyr)
library(stringr)
library(knitr)
library(pheatmap)


wd = "./"
colors <- c("#0571b0", "#ca0020")

Load our data

We first produce a matrix of read counts after aligning to both the Human and Plasmodium falciparum 3D7 reference genome. Subread’s featureCounts program is then used to allocate reads to gene features using the gff file PlasmoDB-12.0_Pfalciparum3D7.gff from PlasmoDB. For both Subread programs the default options are used.

setwd(wd)
# # Next subreads featureCounts was used to allocate reads to genes. This
# was saved for re-use files <-
# Sys.glob('/home/users/allstaff/tonkin-hill.g/all_gene_analysis/alignment/*.sam')
# fc_genes_aligned_w_Pfhuman_withoutVivax <- featureCounts(files, annot.ext
# = './data/PlasmoDB-12.0_Pfalciparum3D7.gff' , isPairedEnd=TRUE,
# isGTFAnnotationFile=TRUE, GTF.attrType='ID', GTF.featureType='gene' ,
# nthreads=15)

# Load gene ID mappings which we use later on.
geneID_mappings <- fread("./data/geneID_mappings.txt", data.table = FALSE, stringsAsFactors = FALSE)
trim <- function(x) gsub("^\\s+|\\s+$", "", x)
s <- str_split(as.character(geneID_mappings$`[Previous ID(s)]`), ",")
geneID_mappings <- data.frame(current = rep(geneID_mappings$`[Gene ID]`, sapply(s, 
    FUN = length)), old = unlist(s))
geneID_mappings$old <- str_trim(geneID_mappings$old)

# Load read counts (if featureCounts has been run previously)
load("./data/fc_genes_with_all_samples_aligned_human_Pf_WithOutVivax_subread_uH.RData")
fc2 <- fc_genes_aligned_w_Pfhuman_withoutVivax
t <- fc2$counts

# Rename samples to something more sensible colnames(t) <-
# gsub('alignment\\.sam','',colnames(t)) colnames(t) <-
# gsub('.*vivax\\.','',colnames(t)) colnames(t) <- gsub('_S.*','',
# colnames(t))
fc2$counts <- t

x <- DGEList(counts = fc2$counts, genes = fc2$annotation)

Initial filter

We next filter out genes that do not have sufficient coverage across our samples for reliable estimates to be made.

setwd(wd)
before <- nrow(x$counts)
keep <- rowSums(cpm(x) > 2) >= 10
x <- x[keep, , keep.lib.sizes = FALSE]

We require that there are at least 2 reads per million for at least 10 samples in order for a gene to be included in the analysis. This reduced the number of genes being considered from 5777 to 4144.

Remove low depth samples

setwd(wd)
bplot <- melt(colSums(x$counts))
colnames(bplot) <- c("Read.Counts")
bplot$Sample <- rownames(bplot)

gg <- ggplot(bplot, aes(x = factor(Sample), y = Read.Counts)) + geom_bar(stat = "identity")
gg <- gg + theme_bw() + scale_y_sqrt(breaks = c(0, 10000, 1e+06, 1e+07, 1e+08))
gg <- gg + theme(axis.text.x = element_text(size = 12, angle = 90), axis.text.y = element_text(size = 12, 
    angle = 0), axis.title = element_text(size = 14, face = "bold"))
gg <- gg + labs(x = "Sample", y = "Read Count")
gg <- gg + geom_hline(aes(yintercept = 1e+06), col = "red")

x$counts <- x$counts[, !grepl("SFD1|SFM9|SFC\\.025", colnames(x$counts))]
filt.annnotation <- fc2$annotation[fc2$annotation$GeneID %in% rownames(x$counts), 
    ]
dge <- DGEList(counts = x$counts, genes = filt.annnotation)

gg

Samples SFD1, SFM9 and SFC.025 were not sequenced to a sufficient depth to be reliable and thus are removed.

Remove drug treated samples

Samples SFU2 and SFU3 were drug treated and are removed. We repeated the analysis of the all gene DGE omitting a few patients who had anti-malarial treatments in preceding months. The patients omitted are: SFC 023, SFM007, IFM 012 and IFM 021.

x$counts <- x$counts[, !grepl("SFU2|SFU\\.3", colnames(x$counts))]
x$counts <- x$counts[, !grepl("SFC\\.023|SFM\\.7|IFM12|IFM21", colnames(x$counts))]
filt.annnotation <- fc2$annotation[fc2$annotation$GeneID %in% rownames(x$counts), 
    ]
dge <- DGEList(counts = x$counts, genes = filt.annnotation)

Now we take the log transform of our sample counts (RPKM) to estimate the proportion of different stages present.

setwd(wd)
our_log_rpkm <- rpkm(dge)
our_log_rpkm <- log2(1 + our_log_rpkm)

Estimate Contributions from Different Life-cycle Stages

Load Data

To estimate the proportion of different life-cycle stages in each of our samples we require a reference data set. Su et al provide such a reference. They performed RNA-seq at two gametocyte stages, an ookinete stage and four time points of erythrocytic stages representing ring, early trophozoite, late trophozoite, and schizont. As we do not expect any ookinete stage parasites we discarded this reference. The data was downloaded from PlasmoDB and as such read counts were reported in RPKM. To handle outlying counts in a sensible manner a log2 transformation of the RPKM values was performed. This was also done for our gene counts. By next fitting a mixture model we can estimate the proportion of different parasite stages that make up our samples.

setwd(wd)
su_rpkm <- read.csv("./data/ rpkm_7SexualAndAsexualLifeStages_suetal.csv", header = TRUE, 
    sep = ",")

# ignore the Ookinete profile as this should be absent from our data.
su_rpkm$Ookinete <- NULL
rownames(su_rpkm) <- su_rpkm$ID
su_rpkm$ID <- NULL

# take the log transform of the data which helps to manage outlier genes.
su_log_rpkm <- log2(1 + su_rpkm)

Mixture Model

Given a set of stages \(S\) and a set of genes \(g_i: i\in \{1,...,N\}\) we want to minimise

\[ \sum_{i=1}^N \left( g_{i,sample} - \sum_{s \in S} \pi_s g_{i,s} \right)^2 \]

Subject to constraints

\[ \sum_{s\in S} \pi_s = 1 \]

\[ \pi_s > 0 \]

Here \(\pi_s\) is proportion of stage \(s\) that is attributed to having contributed to our sample. This model was fit using R’s solve.QP function.

setwd(wd)
findMix <- function(Y, X) {
    X[is.na(X)] <- t(replicate(ncol(X), apply(X, 1, mean, na.rm = T)))[is.na(X)]
    Rinv <- solve(chol(t(X) %*% X))
    C <- cbind(rep(1, ncol(X)), diag(ncol(X)))
    b <- c(1, rep(0, ncol(X)))
    d <- t(Y) %*% X
    qp <- solve.QP(Dmat = Rinv, factorized = TRUE, dvec = d, Amat = C, bvec = b, 
        meq = 1)
    sol <- qp$solution
    sol[sol < 1e-10] <- 0
    return(sol)
}

Calculate Sample Life-Cycle Profiles

We fit this mixture model to each of our samples in turn. The results are then plotted. A column represents each sample in the plot below. As we are fitting proportion parameters each columns values must add to 1 over the 5 stages. Note that we have also combined the estimated proportions for the gametocyte samples into one gametocyte variable. The columns are coloured by phenotype.

setwd(wd)
# First get the intersection of the genes for the two datasets and order
# them by rowname.
inter <- intersect(rownames(our_log_rpkm), rownames(su_log_rpkm))

O <- our_log_rpkm[rownames(our_log_rpkm) %in% inter, ]
O <- O[order(rownames(O)), ]
S <- su_log_rpkm[rownames(su_log_rpkm) %in% inter, ]
S <- S[order(rownames(S)), ]

# Now lets fit some samples!
ourPlotData <- data.frame()
for (i in 1:ncol(O)) {
    mix <- findMix(O[, i], as.matrix(S))
    ourPlotData <- rbind(ourPlotData, data.frame(sample = rep(colnames(O)[i], 
        ncol(S)), stage = colnames(S), proportion = mix))
}

# Organise the results.
ourPlotData$stage <- gsub("Gametocyte.*", "Gametocyte", ourPlotData$stage)
ourPlotData <- aggregate(proportion ~ sample + stage, data = ourPlotData, FUN = sum)
ourPlotData <- within(ourPlotData, stage <- factor(stage, levels = c("Ring", 
    "Early.Trophozoite", "Late.Trophozoite", "Schizont", "Gametocyte")))
ourPlotData$phenotype <- ifelse(substring(ourPlotData$sample, 1, 1) == "I", 
    "non-severe", "severe")

# Make a pretty plot.
gg <- ggplot(ourPlotData, aes(x = factor(sample), y = proportion, fill = factor(phenotype))) + 
    geom_bar(stat = "identity")
gg <- gg + scale_fill_manual(values = c(`non-severe` = "#2c7bb6", severe = "#d7191c"))
gg <- gg + facet_wrap(~stage, ncol = 1)
gg <- gg + theme_bw()
gg <- gg + theme(axis.text.x = element_text(size = 12, angle = 90), axis.text.y = element_text(size = 12, 
    angle = 0), axis.title = element_text(size = 14, face = "bold"), strip.text.x = element_text(size = 16, 
    face = "bold"))
gg <- gg + labs(x = "Sample", y = "Proportion", fill = "Stage")
gg <- gg + theme(legend.text = element_text(size = 14))
gg <- gg + theme(legend.key.size = unit(0.25, "in"))
gg <- gg + theme(legend.title = element_text(size = 16, face = "bold"))
gg <- gg + guides(fill = guide_legend(title = "Phenotype"))
gg

Investigate Differential Expression

We now perform the Voom transformation on our count matrix. Prior to the transformation we use TMM normalisation to account for the different library sizes present in our sample. TMM was chosen as it is more robust to outliers. From the Voom variance trend it is evident that there are a number of genes that have both high variability and high expression. After looking at some of the main offenders these were identified to be influenced by staging in the parasite. Consequently it is important to account for life-cycle stage when conducting the differential expression analysis.

options(width = 150)
setwd(wd)
categories <- as.factor(substring(rownames(dge$samples), 1, 1))
dge <- calcNormFactors(dge, method = "TMM")
dge$samples$group <- categories
design <- model.matrix(~group, data = dge$samples)

v <- voom(dge, design = design, plot = TRUE)

PCA Normalising for Library Size

The PCA plot below indicates that accounting for library size alone does not cope with the impact of life-cycle stages. Notably SFC21 is clearly an outlier and was identified in the mixture model as containing later stage parasites as well as gametocytes. IFM14 is also slightly separate in the PCA plot and was identified as having a proportion of Schizont stage parasite present.

setwd(wd)
plotPCA(v$E, col = colors[categories], cex = 0.8, isLog = TRUE)

Further the Relative Log Expression (RLE) plot below suggests that there is something different about SFC21 as well as highlighting IFM060 as being different.

setwd(wd)
plotVoomRLE <- function(E, colours) {
    mn <- apply(E, 1, median)
    rle <- data.frame(sweep(E, MARGIN = 1, STATS = mn, FUN = "-"))
    boxplot(rle, col = colours, outline = FALSE, las = 2, ylim = c(-7, 7))
    abline(h = 0, col = "black")
}
plotVoomRLE(v$E, colors[categories])

PCA Normalising for Library Size, Ring, Gametocyte and Schizont effects.

To investigate the impact of life-cycle stages in our analysis we fit a linear model using limma’s removeBatchEffect. Initially ring, gametocyte and schizont parameters were fit along with the disease phenotype factor. This was because for the most part the Trophozoite stages could be represented by accounting for these stages as they would be present implicitly in the model.

The PCA indicates that we have dealt with the outlying SFC21 sample as well as other less outlying samples such as IFM14 which showed a proportion of Schizont stage parasites in the mixture model. Unfortunately due to the low number of samples that have proportions of Schizont and Gametocytes estimating differential differential expression in severe disease becomes impossible. This is because there is insufficient data to estimate these stage parameters and consequently the uncertainty in the model is too high to find significant differences between severe and non-severe disease.

setwd(wd)
covs <- data.frame(v$design[, 2])
ourPlotData$phenotype <- NULL
c <- dcast(ourPlotData, sample ~ ..., value.var = "proportion")
covs <- merge(covs, c, by.x = 0, by.y = "sample")

colnames(covs) <- c("sample", "disease", colnames(c)[2:ncol(c)])
rownames(covs) <- covs$sample
covs$sample <- NULL
covs <- covs[match(colnames(v$E), rownames(covs)), ]
stopifnot(colnames(v$E) == rownames(covs))
# head(covs)

covs <- covs[, c(1, 2, 5, 6)]
# head(covs)

mod = model.matrix(as.formula(paste("~", paste(colnames(covs), collapse = " + "), sep = "")), data = covs)

norm_counts_ring <- removeBatchEffect(v$E, covariates = mod[, 3:ncol(mod)], design = mod[, 1:2])
plotPCA(norm_counts_ring, col = colors[categories], cex = 0.8, isLog = TRUE)

The RLE plot also suggests we have dealt with SFC21 however accounting for these stages does not seem to have accounted for the differences we see in the IFM060 sample. The mixture model did not identify IFM060 as being noticeably different from the other samples and consequently it is likely that there is some other unknown factor impacting on its expression.

setwd(wd)
plotVoomRLE(norm_counts_ring, col = colors[categories])

PCA Normalising for Library Size and Ring Stage Effects

We then investigate the impact of only accounting for the Ring stage parameter in the model. This gives us more power with which to identify differential expression related to severe disease. However, from the PCA plot below it is clear that accounting for Ring stage alone is insufficient and fails to adequately deal with SFC21.

setwd(wd)
covs <- covs[, c(1, 2)]

mod = model.matrix(as.formula(paste("~", paste(colnames(covs), collapse = " + "), sep = "")), data = covs)

norm_counts_ring <- removeBatchEffect(v$E, covariates = mod[, 3:ncol(mod)], design = mod[, 1:2])
plotPCA(norm_counts_ring, col = colors[categories], cex = 0.8, isLog = TRUE)

We are however able to identify differentially expressed genes in this less parameterised model. The summary of results accounting only for the Ring stage variable are given below. This test was performed using the limma-Voom pipeline. Ideally we would be able to keep both the power in out tests and account for the remaining unwanted factors. To achieve this we make use of RUV-4 to estimate dummy variables that represent multiple unknown factors of unwanted variation.

setwd(wd)
stopifnot(colnames(dge) == rownames(mod))
v2 <- voom(dge, design = mod, plot = FALSE)
fit <- lmFit(v2, mod)
fit <- eBayes(fit, robust = TRUE)

summary(de1 <- decideTests(fit, adjust.method = "BH", p.value = 0.05))

##    (Intercept) disease Ring
## -1          81      18 1265
## 0          681    4069 1734
## 1         3382      57 1145

Estimate Unwanted Factors of Variation

To cope with the outlier samples such as SFC21 whilst retaining statistical power we estimate factors of unwanted variation using RUV-4.
RUV-4 requires a set of control genes which are believed to be relatively unaffected by the condition of interest, in our case this is disease severity. RUV-4 is however fairly robust to the choice of control genes.
We chose to use the 1000 genes found to have the highest p-values in the experiment of Vignali et al as controls. The experiment of Vignali et al looked at differences in expression between pregnancy associated malaria and childhood malaria. Although this is not the same association we are investigating it was considered close enough to perform adequately as a source of control genes. Further an analysis using SVA which does not require controls and rather estimates them empirically was found to produce similar results with only 5 out of 119 genes found using SVA missing from the RUV-4 approach. Further RUV-4 attempts to recover some variation that may be lost in the vanilla SVA approach when the factor of interest (severe disease) correlates with an unwanted factor. Consequently it leads to a higher number of differentially expressed genes being found. It was also thought that having an independently sourced set of control genes was preferable to empirically deriving such a set.

setwd(wd)
contol_genes_vignali <- read.table("./data/contol_genes_vignali.txt", quote = "\"")

ctrl_vignali <- geneID_mappings$current[geneID_mappings$old %in% contol_genes_vignali$V1]
length(ctrl_vignali)

## [1] 1009

empirical_controls <- ctrl_vignali[0:length(ctrl_vignali)]
empirical_controls <- rownames(v$E) %in% empirical_controls

categoriesRUV <- categories
categoriesRUV <- data.matrix(as.numeric(categoriesRUV == "S"))
ring <- data.matrix(mod[, c(1, 3)])
genes <- data.matrix(t(v$E))

ruv <- RUV4(genes, categoriesRUV, empirical_controls, 3, Z = ring)

modRUV = cbind(mod, ruv$W)

norm_counts_ring_ruv <- removeBatchEffect(v$E, covariates = modRUV[, 3:ncol(modRUV)], design = modRUV[, 1:2])

Note that although we used 1000 genes from the experiment of Vignali et al only 533 were found in our reduced expression matrix.

The PCA plot below indicates that we have dealt with most of the problems due to staging. Here we have included the Ring stage proportion from the mixture model as well as three factors of unwanted variation estimated using RUV-4.

setwd(wd)
plotPCA(norm_counts_ring_ruv, col = colors[categories], cex = 0.8, isLog = TRUE)

The RLE plot also indicates that we have succesfully dealt with most of the staging issues. Both SFC21 and IFM14 have reasonable box plots. Moreover, IFM060 has a nicer boxplot indicating that in using RUV-4, not only have we dealt with staging issues, we have also accounted for some other unknown confounding factors that would have impacted our results. The variation in each sample has also been reduced which is indicated in the reduced height of the boxplot whiskers. Finally, the results were found to be relatively robust to the removal of the outlier samples such as SFC21 and IFM14. Consequently, this approach seems to succesfully deal with both life-cycle staging issues and other unknown impacting factors.

setwd(wd)
plotVoomRLE(norm_counts_ring_ruv, colors[categories])

Identify DE Genes using Limma and Voom

We now use the limma-voom pipeline, with the robust ebayes option which handles dispersion outliers. This was done to further ensure our results were less likely to be affected by outlier samples. Multiple testing correction was performed using the Benjamini-Hochberg approach.

setwd(wd)
stopifnot(colnames(dge) == rownames(modRUV))
v2 <- voom(dge, design = modRUV, plot = F)
fit <- lmFit(v2, modRUV)
fit <- eBayes(fit, robust = TRUE)
s <- summary(de2 <- decideTests(fit, adjust.method = "BH", p.value = 0.05))
s

##    (Intercept) disease Ring               
## -1          91      72 1393 1621 1101  478
## 0          548    4033 1450 1651 2070 3114
## 1         3505      39 1301  872  973  552

Overall 111 genes were found to be differentially expressed between severe and non-severe cases of malaria with a false dicovery rate threshold of 0.05.

A good check for validity of our model it to look at the distribution of the resulting p-values. If everything is okay we would expect a uniform distribution except near \(p=0\) where we would hope to see a spike. The barplot below indicates this is what we see which is helpful in affirming that we have done okay in removing unwanted variation without negatively impacting on the variation due to the variable of interest (diseas severity).

setwd(wd)
top_ring_ruv <- topTable(fit, coef = 2, p.value = 0.1, sort.by = "p", number = Inf, adjust.method = "BH", confint = TRUE)
hist <- data.frame(topTable(fit, coef = 2, number = Inf))
gg <- ggplot(hist, aes(x = P.Value)) + geom_histogram(binwidth = 0.01)
gg <- gg + theme_bw()
gg <- gg + theme(axis.text.x = element_text(size = 12), axis.text.y = element_text(size = 12, angle = 0), axis.title = element_text(size = 12, face = "bold"))
gg <- gg + labs(x = "P value", y = "Count")
gg

Results table

Below is a table of genes that were found to be differentially expressed, ordered by their respective p-values. The 95% confidence intervals are given with the estimated LFC as well as the BH adjusted p-values and the log-odds that the gene is differentially expressed. Here we report for interest sake all genes up to a adjusted p-value threshold of 0.1.

setwd(wd)
# Load additional gene information
GeneAnnotationPlasmoDB <- fread("./data/GeneAnnotationPlasmoDB.txt", data.table = FALSE, na.strings = "N/A")

# First lets import some additional gene information to make a nicer table
GeneAnnotationPlasmoDB <- GeneAnnotationPlasmoDB[, colnames(GeneAnnotationPlasmoDB) %in% c("[Gene ID]", "[Product Description]", "[Gene Name or Symbol]")]
top_ring_ruv <- merge(top_ring_ruv, GeneAnnotationPlasmoDB, by.x = 0, by.y = "[Gene ID]", all.x = TRUE)
top_ring_ruv <- top_ring_ruv[with(top_ring_ruv, order(adj.P.Val)), ]

# Now print the table
top_ring_ruv$P.Value <- format(top_ring_ruv$P.Value, scientific = TRUE, digits = 3)
top_ring_ruv$adj.P.Val <- format(top_ring_ruv$adj.P.Val, scientific = TRUE, digits = 3)
kable(top_ring_ruv[, c(2:4, 6:ncol(top_ring_ruv))], digits = 3)

	GeneID	Chr	Start	Strand	Length	logFC	CI.L	CI.R	AveExpr	t	P.Value	adj.P.Val	B	[Product Description]	[Gene Name or Symbol]
9	PF3D7_0115700	Pf3D7_01_v3	607390	-	7504	-1.695	-2.671	-0.718	4.472	-5.551	2.64e-06	5.48e-03	4.608	erythrocyte membrane protein 1, PfEMP1	VAR
14	PF3D7_0202000	Pf3D7_02_v3	103385	-	2412	-2.232	-3.132	-1.331	14.042	-5.745	2.34e-06	5.48e-03	4.793	knob-associated histidine-rich protein	KAHRP
271	PF3D7_1255200	Pf3D7_12_v3	2241271	-	7692	-1.490	-2.030	-0.951	4.566	-5.412	4.07e-06	5.63e-03	4.220	erythrocyte membrane protein 1, PfEMP1	VAR
23	PF3D7_0223500	Pf3D7_02_v3	916352	-	7297	-1.139	-1.932	-0.345	5.205	-4.963	1.63e-05	8.42e-03	2.968	erythrocyte membrane protein 1, PfEMP1	VAR
31	PF3D7_0316600	Pf3D7_03_v3	669302	-	1572	-1.407	-1.944	-0.870	10.248	-5.170	9.43e-06	8.42e-03	3.434	formate-nitrite transporter	FNT
37	PF3D7_0400100	Pf3D7_04_v3	28706	+	8972	-1.593	-1.921	-1.266	4.810	-5.026	1.34e-05	8.42e-03	3.139	erythrocyte membrane protein 1, PfEMP1	VAR
156	PF3D7_0900100	Pf3D7_09_v3	20080	+	7806	-1.462	-2.010	-0.915	4.673	-5.057	1.22e-05	8.42e-03	3.224	erythrocyte membrane protein 1, PfEMP1	VAR
189	PF3D7_1023600	Pf3D7_10_v3	987358	-	2791	-2.045	-3.030	-1.060	-0.122	-4.980	1.54e-05	8.42e-03	2.487	conserved Plasmodium protein, unknown function	NA
243	PF3D7_1223900	Pf3D7_12_v3	972710	-	684	-2.228	-4.701	0.246	2.658	-4.936	1.86e-05	8.58e-03	2.764	50S ribosomal protein L24, putative	NA
142	PF3D7_0809100	Pf3D7_08_v3	459312	+	7256	-1.773	-3.635	0.089	3.226	-4.884	2.08e-05	8.60e-03	2.665	erythrocyte membrane protein 1, PfEMP1	VAR
4	PF3D7_0106000	Pf3D7_01_v3	255775	-	2769	1.185	0.199	2.172	1.476	4.664	4.07e-05	1.23e-02	1.920	conserved Plasmodium protein, unknown function	NA
36	PF3D7_0324900	Pf3D7_03_v3	1030822	-	7433	-1.274	-2.295	-0.254	3.988	-4.507	6.54e-05	1.23e-02	1.680	erythrocyte membrane protein 1, PfEMP1	VAR
40	PF3D7_0404600	Pf3D7_04_v3	247731	+	12417	-1.457	-1.770	-1.145	7.604	-4.502	7.43e-05	1.23e-02	1.515	conserved Plasmodium membrane protein, unknown function	NA
45	PF3D7_0412700	Pf3D7_04_v3	561667	-	7676	-1.440	-2.188	-0.692	4.841	-4.530	6.09e-05	1.23e-02	1.753	erythrocyte membrane protein 1, PfEMP1	VAR
85	PF3D7_0600600	Pf3D7_06_v3	29618	-	1867	-1.681	-2.462	-0.901	3.049	-4.700	3.63e-05	1.23e-02	2.155	erythrocyte membrane protein 1 (PfEMP1), exon 2	VAR
105	PF3D7_0632800	Pf3D7_06_v3	1374797	-	7831	-1.240	-1.577	-0.904	4.681	-4.544	5.85e-05	1.23e-02	1.791	erythrocyte membrane protein 1, PfEMP1	VAR
107	PF3D7_0703100	Pf3D7_07_v3	121414	+	543	0.985	0.194	1.777	3.582	4.477	7.15e-05	1.23e-02	1.588	conserved Plasmodium protein, unknown function	NA
120	PF3D7_0712600	Pf3D7_07_v3	566726	-	7583	-1.748	-2.417	-1.079	3.429	-4.685	3.80e-05	1.23e-02	2.144	erythrocyte membrane protein 1, PfEMP1	VAR
133	PF3D7_0800100	Pf3D7_08_v3	21361	+	7293	-1.596	-2.257	-0.936	4.508	-4.513	6.58e-05	1.23e-02	1.687	erythrocyte membrane protein 1, PfEMP1	VAR
136	PF3D7_0802000	Pf3D7_08_v3	146089	+	4194	-1.266	-1.753	-0.778	9.188	-4.509	6.90e-05	1.23e-02	1.558	glutamate dehydrogenase, putative	GDH3
175	PF3D7_1000100	Pf3D7_10_v3	28490	+	7675	-1.339	-1.639	-1.040	4.505	-4.569	5.41e-05	1.23e-02	1.861	erythrocyte membrane protein 1, PfEMP1	VAR
204	PF3D7_1105100	Pf3D7_11_v3	226065	+	354	-1.063	-1.589	-0.536	9.705	-4.600	5.10e-05	1.23e-02	1.799	histone H2B	H2B
216	PF3D7_1123100	Pf3D7_11_v3	909366	+	6959	-0.597	-0.908	-0.287	9.103	-4.524	6.21e-05	1.23e-02	1.610	calcium-dependent protein kinase 7	CDPK7
231	PF3D7_1200100	Pf3D7_12_v3	16973	+	7525	-1.592	-2.227	-0.957	4.052	-4.609	4.80e-05	1.23e-02	1.964	erythrocyte membrane protein 1, PfEMP1	VAR
296	PF3D7_1344800	Pf3D7_13_v3	1796274	+	1436	-0.768	-1.123	-0.413	6.260	-4.560	5.58e-05	1.23e-02	1.803	aspartate carbamoyltransferase	ATCase
248	PF3D7_1228800	Pf3D7_12_v3	1169557	-	9630	-0.657	-1.727	0.414	6.788	-4.415	8.63e-05	1.38e-02	1.365	WD repeat-containing protein, putative	NA
84	PF3D7_0532400	Pf3D7_05_v3	1312471	+	1684	-1.315	-1.774	-0.856	8.118	-4.393	9.77e-05	1.40e-02	1.251	lysine-rich membrane-associated PHISTb protein	LyMP
102	PF3D7_0626200	Pf3D7_06_v3	1058666	-	1257	1.643	0.966	2.319	2.878	4.387	9.37e-05	1.40e-02	1.321	conserved Plasmodium protein, unknown function	NA
244	PF3D7_1224000	Pf3D7_12_v3	974372	+	1170	-1.670	-3.718	0.378	2.666	-4.378	9.63e-05	1.40e-02	1.298	GTP cyclohydrolase I	GCH1
322	PF3D7_1414200	Pf3D7_14_v3	564024	-	1224	0.818	0.286	1.349	5.924	4.353	1.04e-04	1.43e-02	1.233	conserved Plasmodium protein, unknown function	NA
198	PF3D7_1100100	Pf3D7_11_v3	24160	+	7439	-1.288	-1.828	-0.748	4.713	-4.310	1.18e-04	1.58e-02	1.148	erythrocyte membrane protein 1, PfEMP1	VAR
6	PF3D7_0109700	Pf3D7_01_v3	379149	-	658	-1.423	-2.847	0.001	4.127	-4.269	1.33e-04	1.73e-02	1.040	rRNA biogenesis protein RRP36, putative	RRP36
71	PF3D7_0519500	Pf3D7_05_v3	801450	-	7678	-0.942	-1.573	-0.311	7.017	-4.157	1.86e-04	2.09e-02	0.640	carbon catabolite repressor protein 4, putative	CCR4
153	PF3D7_0830300	Pf3D7_08_v3	1290240	-	1167	1.591	1.299	1.884	2.023	4.162	1.83e-04	2.09e-02	0.694	sporozoite invasion-associated protein 2	SIAP2
168	PF3D7_0925300	Pf3D7_09_v3	1019164	-	1740	2.109	1.367	2.850	0.173	4.158	1.86e-04	2.09e-02	0.535	proline–tRNA ligase, putative	aPRS
193	PF3D7_1028000	Pf3D7_10_v3	1160031	+	3391	-0.991	-1.656	-0.326	6.363	-4.158	1.86e-04	2.09e-02	0.667	methyltransferase, putative	NA
285	PF3D7_1316600	Pf3D7_13_v3	691014	+	3112	-1.262	-1.567	-0.958	6.456	-4.192	1.76e-04	2.09e-02	0.726	choline-phosphate cytidylyltransferase	CCT
117	PF3D7_0711700	Pf3D7_07_v3	511950	-	7476	-1.151	-1.908	-0.394	4.402	-4.081	2.34e-04	2.50e-02	0.533	erythrocyte membrane protein 1, PfEMP1	VAR
287	PF3D7_1318300	Pf3D7_13_v3	753910	+	5523	-1.051	-1.390	-0.712	5.766	-4.078	2.36e-04	2.50e-02	0.476	conserved Plasmodium protein, unknown function	NA
166	PF3D7_0917800	Pf3D7_09_v3	734629	+	1314	1.808	1.549	2.068	1.383	4.051	2.55e-04	2.64e-02	0.378	conserved Plasmodium protein, unknown function	NA
58	PF3D7_0500100	Pf3D7_05_v3	20929	+	7528	-1.287	-1.826	-0.748	3.399	-4.023	2.77e-04	2.68e-02	0.384	erythrocyte membrane protein 1, PfEMP1	VAR
224	PF3D7_1135300	Pf3D7_11_v3	1381015	-	1230	1.219	0.684	1.754	2.281	4.032	2.70e-04	2.68e-02	0.380	conserved Plasmodium membrane protein, unknown function	NA
238	PF3D7_1213100	Pf3D7_12_v3	576417	-	164	-2.305	-2.853	-1.757	2.312	-4.036	2.79e-04	2.68e-02	0.339	U1 spliceosomal RNA	NA
286	PF3D7_1316900	Pf3D7_13_v3	701047	-	2877	0.669	0.039	1.299	7.752	4.007	2.90e-04	2.73e-02	0.185	conserved Plasmodium protein, unknown function	NA
242	PF3D7_1223400	Pf3D7_12_v3	941125	+	5621	-0.766	-2.537	1.005	11.206	-3.995	3.01e-04	2.77e-02	0.101	phospholipid-transporting ATPase, putative	NA
124	PF3D7_0713600	Pf3D7_07_v3	617933	+	2935	1.165	0.776	1.554	3.264	3.969	3.24e-04	2.92e-02	0.245	mitochondrial ribosomal protein S5 precursor, putative	NA
41	PF3D7_0404900	Pf3D7_04_v3	267244	-	1137	1.903	1.310	2.495	3.340	3.976	3.31e-04	2.92e-02	0.231	6-cysteine protein	P41
65	PF3D7_0509000	Pf3D7_05_v3	376855	-	1598	-0.641	-1.129	-0.152	5.782	-3.938	3.55e-04	2.94e-02	0.094	SNAP protein (soluble N-ethylmaleimide-sensitive factor attachment protein), putative	NA
143	PF3D7_0810800	Pf3D7_08_v3	548200	+	2417	-1.107	-1.926	-0.288	7.387	-3.954	3.49e-04	2.94e-02	0.064	hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase	PPPK-DHPS
275	PF3D7_1303000	Pf3D7_13_v3	158144	+	635	-1.133	-2.435	0.170	3.355	-3.939	3.54e-04	2.94e-02	0.170	conserved Plasmodium protein, unknown function	NA
139	PF3D7_0805600	Pf3D7_08_v3	312034	+	927	0.774	0.335	1.213	7.188	3.895	4.02e-04	3.22e-02	-0.097	PAP2-like protein, putative	NA
315	PF3D7_1400100	Pf3D7_14_v3	1393	+	3951	-1.321	-1.729	-0.913	4.966	-3.901	4.04e-04	3.22e-02	0.021	erythrocyte membrane protein 1 (PfEMP1), pseudogene	NA
251	PF3D7_1230500	Pf3D7_12_v3	1253973	-	1509	0.909	-0.278	2.097	4.436	3.879	4.22e-04	3.30e-02	-0.002	WD repeat-containing protein, putative	NA
24	PF3D7_0300100	Pf3D7_03_v3	36965	+	7518	-1.134	-1.505	-0.762	4.351	-3.865	4.39e-04	3.32e-02	-0.035	erythrocyte membrane protein 1, PfEMP1	VAR
265	PF3D7_1246600	Pf3D7_12_v3	1936522	+	1173	-0.852	-1.815	0.111	5.347	-3.864	4.40e-04	3.32e-02	-0.078	pre-mRNA-splicing factor CWC26, putative	BUD13
7	PF3D7_0113000	Pf3D7_01_v3	487892	-	2236	-1.480	-3.080	0.121	11.345	-3.858	5.27e-04	3.64e-02	-0.387	glutamic acid-rich protein	GARP
237	PF3D7_1212800	Pf3D7_12_v3	565966	+	966	1.021	0.421	1.621	2.457	3.805	5.22e-04	3.64e-02	-0.185	iron-sulfur subunit of succinate dehydrogenase	NA
260	PF3D7_1240900	Pf3D7_12_v3	1735543	+	7866	-1.406	-2.440	-0.371	4.296	-3.816	5.12e-04	3.64e-02	-0.165	erythrocyte membrane protein 1, PfEMP1	VAR
267	PF3D7_1249000	Pf3D7_12_v3	2005175	-	2019	1.002	0.352	1.652	1.154	3.821	4.98e-04	3.64e-02	-0.189	conserved Plasmodium membrane protein, unknown function	NA
347	PF3D7_1457000	Pf3D7_14_v3	2336649	-	2505	-0.648	-1.396	0.101	8.961	-3.813	5.11e-04	3.64e-02	-0.374	signal peptide peptidase	SPP
83	PF3D7_0532300	Pf3D7_05_v3	1308278	+	1663	-1.199	-1.939	-0.459	10.800	-3.818	5.46e-04	3.65e-02	-0.417	Plasmodium exported protein (PHISTb), unknown function	NA
316	PF3D7_1401400	Pf3D7_14_v3	53411	-	324	-0.853	-1.218	-0.488	12.466	-3.797	5.42e-04	3.65e-02	-0.445	early transcribed membrane protein 14.1	ETRAMP14
111	PF3D7_0704600	Pf3D7_07_v3	216024	-	13049	-0.663	-1.466	0.140	10.228	-3.766	5.84e-04	3.78e-02	-0.524	E3 ubiquitin-protein ligase	UT
205	PF3D7_1105300	Pf3D7_11_v3	231847	-	2392	1.352	1.003	1.700	1.696	3.767	5.82e-04	3.78e-02	-0.299	conserved Plasmodium protein, unknown function	NA
211	PF3D7_1118400	Pf3D7_11_v3	699869	-	921	1.065	0.445	1.685	3.280	3.756	6.02e-04	3.84e-02	-0.298	haloacid dehalogenase-like hydrolase, putative	NA
262	PF3D7_1244200	Pf3D7_12_v3	1852844	-	2838	1.031	0.729	1.333	5.481	3.739	6.32e-04	3.97e-02	-0.420	RNA polymerase II transcription factor B subunit 2, putative	TFB2
54	PF3D7_0419800	Pf3D7_04_v3	874811	-	711	0.644	0.109	1.179	5.924	3.733	6.43e-04	3.98e-02	-0.460	60S ribosomal protein L7ae/L30e, putative	NA
13	PF3D7_0201900	Pf3D7_02_v3	91318	-	7521	-1.527	-2.211	-0.843	10.614	-3.763	6.87e-04	4.12e-02	-0.612	erythrocyte membrane protein 3	EMP3
146	PF3D7_0821500	Pf3D7_08_v3	967901	-	840	0.820	0.569	1.070	4.918	3.706	6.94e-04	4.12e-02	-0.471	ribosomal RNA small subunit methyltransferase NEP1, putative	NEP1
147	PF3D7_0822200	Pf3D7_08_v3	982570	+	5127	1.108	0.550	1.666	2.942	3.700	7.07e-04	4.12e-02	-0.438	conserved Plasmodium membrane protein, unknown function	NA
149	PF3D7_0823800	Pf3D7_08_v3	1043813	+	1968	-0.753	-1.486	-0.020	5.245	-3.700	7.05e-04	4.12e-02	-0.518	DnaJ protein, putative	NA
51	PF3D7_0417400	Pf3D7_04_v3	756294	+	20310	-0.792	-1.152	-0.432	8.067	-3.685	7.37e-04	4.24e-02	-0.703	conserved Plasmodium protein, unknown function	NA
121	PF3D7_0712800	Pf3D7_07_v3	581386	-	7538	-1.348	-2.079	-0.616	4.007	-3.677	7.57e-04	4.24e-02	-0.508	erythrocyte membrane protein 1, PfEMP1	VAR
154	PF3D7_0831700	Pf3D7_08_v3	1365467	-	2040	-0.982	-1.261	-0.702	13.434	-3.690	7.53e-04	4.24e-02	-0.742	heat shock protein 70	HSP70-x
1	mal_rna_11:rRNA	M76611	1916	-	108	-1.640	-2.203	-1.077	1.870	-3.641	8.35e-04	4.27e-02	-0.606	NA	NA
25	PF3D7_0302800	Pf3D7_03_v3	148046	-	1260	1.163	0.554	1.772	5.270	3.630	8.76e-04	4.27e-02	-0.700	conserved Plasmodium protein, unknown function	NA
47	PF3D7_0413900	Pf3D7_04_v3	623168	-	3059	-0.742	-1.627	0.143	6.964	-3.656	8.01e-04	4.27e-02	-0.736	ubiquitin carboxyl-terminal hydrolase 13, putative	USP13
57	PF3D7_0423800	Pf3D7_04_v3	1076347	+	1188	2.290	1.835	2.746	2.134	3.628	9.24e-04	4.27e-02	-0.670	cysteine-rich protective antigen	CyRPA
68	PF3D7_0512000	Pf3D7_05_v3	527639	+	1028	-1.030	-1.691	-0.369	5.218	-3.609	9.15e-04	4.27e-02	-0.741	prefoldin subunit 6, putative	NA
81	PF3D7_0529000	Pf3D7_05_v3	1186787	-	2160	0.470	-0.311	1.252	7.651	3.631	8.60e-04	4.27e-02	-0.831	conserved Plasmodium protein, unknown function	NA
103	PF3D7_0629600	Pf3D7_06_v3	1218307	+	945	0.546	0.103	0.988	4.979	3.605	9.25e-04	4.27e-02	-0.734	conserved Plasmodium protein, unknown function	NA
116	PF3D7_0711200	Pf3D7_07_v3	495238	+	3003	1.222	0.659	1.785	2.256	3.636	8.47e-04	4.27e-02	-0.603	conserved Plasmodium protein, unknown function	NA
132	PF3D7_0733000	Pf3D7_07_v3	1417588	-	8647	-1.043	-1.615	-0.471	4.926	-3.623	8.79e-04	4.27e-02	-0.686	erythrocyte membrane protein 1, PfEMP1	VAR
161	PF3D7_0909600	Pf3D7_09_v3	433238	-	2136	1.511	1.178	1.843	0.836	3.642	8.34e-04	4.27e-02	-0.635	conserved Plasmodium protein, unknown function	NA
197	PF3D7_1041300	Pf3D7_10_v3	1642401	-	7548	-1.101	-1.727	-0.474	4.981	-3.628	8.68e-04	4.27e-02	-0.674	erythrocyte membrane protein 1, PfEMP1	VAR
213	PF3D7_1121100	Pf3D7_11_v3	794254	-	5308	-0.793	-1.429	-0.157	8.461	-3.604	9.27e-04	4.27e-02	-0.914	conserved Plasmodium protein, unknown function	NA
298	PF3D7_1346200	Pf3D7_13_v3	1845878	-	507	2.002	1.693	2.312	0.978	3.614	9.19e-04	4.27e-02	-0.701	nuclear import protein MOG1, putative	NA
326	PF3D7_1421150	Pf3D7_14_v3	875173	-	149	-1.649	-2.239	-1.059	1.022	-3.645	8.26e-04	4.27e-02	-0.626	C/D small nucleolar RNA	NA
337	PF3D7_1444800	Pf3D7_14_v3	1844041	-	1577	-0.692	-1.263	-0.122	10.290	-3.622	8.81e-04	4.27e-02	-0.901	fructose-bisphosphate aldolase	FBPA
346	PF3D7_1451800	Pf3D7_14_v3	2123461	+	3139	-0.690	-1.189	-0.190	4.615	-3.616	8.96e-04	4.27e-02	-0.702	sortilin	NA
207	PF3D7_1108700	Pf3D7_11_v3	373238	-	1623	0.745	0.222	1.267	6.854	3.584	9.81e-04	4.47e-02	-0.904	heat shock protein DnaJ homologue Pfj2	NA
95	PF3D7_0617200	Pf3D7_06_v3	717050	+	1868	-1.064	-2.315	0.188	7.853	-3.587	1.03e-03	4.57e-02	-0.992	conserved Plasmodium protein, unknown function	NA
299	PF3D7_1346400	Pf3D7_13_v3	1852898	+	17967	-0.706	-0.963	-0.449	7.849	-3.569	1.02e-03	4.57e-02	-1.005	conserved Plasmodium protein, unknown function	NA
259	PF3D7_1240600	Pf3D7_12_v3	1719574	+	7883	-1.224	-1.818	-0.629	3.851	-3.554	1.07e-03	4.66e-02	-0.814	erythrocyte membrane protein 1, PfEMP1	VAR
303	PF3D7_1354300	Pf3D7_13_v3	2164239	-	3178	-0.517	-1.135	0.102	9.432	-3.556	1.06e-03	4.66e-02	-1.078	large subunit rRNA methyltransferase, putative	NA
220	PF3D7_1126300	Pf3D7_11_v3	1026976	+	2569	1.067	0.818	1.316	4.596	3.543	1.10e-03	4.76e-02	-0.877	DnaJ protein, putative	NA
62	PF3D7_0503100	Pf3D7_05_v3	127064	-	1614	-1.336	-1.742	-0.929	2.177	-3.504	1.23e-03	4.80e-02	-0.920	4-diphosphocytidyl-2-C-methyl-D-erythritol kinase, putative	IspE
99	PF3D7_0622700	Pf3D7_06_v3	916000	-	1300	1.532	0.053	3.011	1.425	3.534	1.13e-03	4.80e-02	-0.858	conserved Plasmodium membrane protein, unknown function	NA
128	PF3D7_0719500	Pf3D7_07_v3	854652	-	2003	0.995	0.204	1.786	1.461	3.509	1.21e-03	4.80e-02	-0.921	LEM3/CDC50 family protein, putative	NA
170	PF3D7_0928500	Pf3D7_09_v3	1146239	-	959	-1.164	-2.209	-0.119	2.608	-3.509	1.21e-03	4.80e-02	-0.908	conserved Plasmodium protein, unknown function	NA
177	PF3D7_1003900	Pf3D7_10_v3	177921	+	950	1.677	0.884	2.470	0.332	3.524	1.16e-03	4.80e-02	-0.924	conserved Plasmodium protein, unknown function	NA
180	PF3D7_1012000	Pf3D7_10_v3	463493	+	3514	-0.679	-1.272	-0.085	6.052	-3.496	1.26e-03	4.80e-02	-1.090	E3 ubiquitin-protein ligase, putative	NA
202	PF3D7_1102800	Pf3D7_11_v3	131703	-	285	-0.910	-1.825	0.006	13.470	-3.540	1.15e-03	4.80e-02	-1.138	early transcribed membrane protein 11.2	ETRAMP11.2
288	PF3D7_1321600	Pf3D7_13_v3	897716	+	3329	1.398	0.495	2.301	0.132	3.515	1.19e-03	4.80e-02	-0.956	phosphodiesterase gamma, putative	PDEgamma
310	PF3D7_1365600	Pf3D7_13_v3	2621261	+	2740	0.733	-0.151	1.617	4.139	3.495	1.26e-03	4.80e-02	-0.967	DNA topoisomerase VI, b subunit, putative	NA
331	PF3D7_1428100	Pf3D7_14_v3	1098038	-	1914	0.966	0.460	1.473	3.882	3.497	1.26e-03	4.80e-02	-0.959	WW domain-binding protein 11, putative	NA
341	PF3D7_1446900	Pf3D7_14_v3	1924425	-	2226	0.763	0.448	1.079	6.864	3.500	1.24e-03	4.80e-02	-1.127	glutaminyl-peptide cyclotransferase, putative	NA
349	PF3D7_1457900	Pf3D7_14_v3	2375579	+	10368	-0.756	-1.417	-0.094	5.650	-3.528	1.15e-03	4.80e-02	-0.978	conserved Plasmodium protein, unknown function	NA
356	PF3D7_1470200	Pf3D7_14_v3	2877586	-	1163	-0.675	-1.356	0.006	5.398	-3.515	1.19e-03	4.80e-02	-0.983	conserved Plasmodium protein, unknown function	NA
138	PF3D7_0804900	Pf3D7_08_v3	279711	-	1476	0.919	-0.323	2.160	5.949	3.480	1.32e-03	4.96e-02	-1.116	GTPase-activating protein, putative	NA
338	PF3D7_1445600	Pf3D7_14_v3	1871778	+	2604	0.679	0.247	1.112	8.272	3.476	1.33e-03	4.97e-02	-1.260	RNA-binding protein, putative	NA
127	PF3D7_0717600	Pf3D7_07_v3	758720	-	4158	-1.473	-1.889	-1.056	3.059	-3.474	1.36e-03	5.02e-02	-1.008	conserved Plasmodium protein, unknown function	NA
73	PF3D7_0522300	Pf3D7_05_v3	902613	-	2232	-0.572	-1.174	0.030	6.700	-3.459	1.39e-03	5.09e-02	-1.227	S-adenosylmethionine-dependent methyltransferase, putative	NA
343	PF3D7_1449900	Pf3D7_14_v3	2044007	-	1023	1.308	0.758	1.858	2.638	3.457	1.40e-03	5.09e-02	-1.031	conserved Plasmodium protein, unknown function	NA
148	PF3D7_0823200	Pf3D7_08_v3	1022629	-	1218	-0.619	-0.974	-0.264	9.617	-3.453	1.42e-03	5.12e-02	-1.351	RNA-binding protein, putative	NA
335	PF3D7_1437800	Pf3D7_14_v3	1530276	-	555	1.770	1.086	2.453	2.830	3.457	1.44e-03	5.16e-02	-1.054	trafficking protein particle complex subunit 5, putative	TRAPPC5
28	PF3D7_0305000	Pf3D7_03_v3	234058	-	1277	0.947	0.074	1.820	3.438	3.441	1.47e-03	5.16e-02	-1.086	elongation factor Ts	EF-Ts
209	PF3D7_1111300	Pf3D7_11_v3	442959	-	870	0.841	0.548	1.135	2.945	3.438	1.48e-03	5.16e-02	-1.079	SNARE protein, putative	GS27
305	PF3D7_1355700	Pf3D7_13_v3	2206592	-	3867	1.237	0.365	2.109	7.278	3.465	1.48e-03	5.16e-02	-1.296	NLI interacting factor-like phosphatase, putative	NIF3
19	PF3D7_0216000	Pf3D7_02_v3	658636	+	5994	-2.074	-2.621	-1.528	0.535	-3.431	1.53e-03	5.29e-02	-1.141	DEAD/DEAH box helicase, putative	NA
53	PF3D7_0419500	Pf3D7_04_v3	866501	-	1611	1.223	0.163	2.283	3.890	3.421	1.55e-03	5.30e-02	-1.144	conserved Plasmodium membrane protein, unknown function	NA
114	PF3D7_0708500	Pf3D7_07_v3	385583	-	2739	-0.737	-1.370	-0.105	6.652	-3.415	1.58e-03	5.35e-02	-1.337	heat shock protein 86 family protein	NA
69	PF3D7_0513600	Pf3D7_05_v3	574941	-	3565	-1.045	-1.363	-0.726	5.614	-3.413	1.61e-03	5.39e-02	-1.283	deoxyribodipyrimidine photo-lyase, putative	NA
210	PF3D7_1115200	Pf3D7_11_v3	576773	+	3504	-0.659	-1.554	0.236	8.247	-3.404	1.63e-03	5.39e-02	-1.445	histone-lysine N-methyltransferase SET7	SET7
229	PF3D7_1145500	Pf3D7_11_v3	1807359	+	2772	1.102	0.252	1.951	1.564	3.404	1.63e-03	5.39e-02	-1.163	ABC transporter B family member 3, putative	ABCB3
59	PF3D7_0501300	Pf3D7_05_v3	68930	+	1184	-0.925	-1.601	-0.250	12.486	-3.399	1.71e-03	5.59e-02	-1.517	skeleton-binding protein 1	SBP1
246	PF3D7_1225600	Pf3D7_12_v3	1035261	-	2895	-0.478	-2.453	1.498	8.007	-3.386	1.71e-03	5.59e-02	-1.485	conserved Plasmodium protein, unknown function	NA
324	PF3D7_1417600	Pf3D7_14_v3	730694	-	13989	-0.568	-1.358	0.222	8.915	-3.382	1.73e-03	5.59e-02	-1.523	conserved Plasmodium protein, unknown function	NA
297	PF3D7_1345200	Pf3D7_13_v3	1812220	-	1710	1.084	0.716	1.452	3.402	3.379	1.74e-03	5.59e-02	-1.227	rhomboid protease ROM6, putative	ROM6
29	PF3D7_0310800	Pf3D7_03_v3	464662	+	330	0.487	-0.214	1.187	6.132	3.360	1.84e-03	5.68e-02	-1.439	conserved Plasmodium protein, unknown function	NA
122	PF3D7_0712900	Pf3D7_07_v3	590326	-	7408	-1.100	-1.332	-0.869	4.206	-3.367	1.80e-03	5.68e-02	-1.294	erythrocyte membrane protein 1, PfEMP1	VAR
190	PF3D7_1025000	Pf3D7_10_v3	1045608	-	4153	-0.570	-0.985	-0.156	8.252	-3.366	1.80e-03	5.68e-02	-1.534	formin 2, putative	NA
212	PF3D7_1119200	Pf3D7_11_v3	722717	-	573	-1.038	-1.443	-0.632	3.783	-3.361	1.83e-03	5.68e-02	-1.279	conserved protein, unknown function	NA
218	PF3D7_1124800	Pf3D7_11_v3	976880	-	1057	-0.568	-1.158	0.023	6.670	-3.363	1.82e-03	5.68e-02	-1.469	nuclear preribosomal assembly protein, putative	NA
234	PF3D7_1206300	Pf3D7_12_v3	281020	-	8283	-1.407	-1.752	-1.062	1.456	-3.354	1.87e-03	5.73e-02	-1.280	conserved Plasmodium protein, unknown function	NA
50	PF3D7_0416100	Pf3D7_04_v3	706529	+	2481	-0.909	-1.422	-0.396	4.248	-3.345	1.91e-03	5.78e-02	-1.360	glutamyl-tRNA(Gln) amidotransferase subunit A	GATA
106	PF3D7_0700100	Pf3D7_07_v3	20307	+	7777	-1.044	-1.871	-0.217	5.158	-3.344	1.93e-03	5.78e-02	-1.411	erythrocyte membrane protein 1, PfEMP1	VAR
203	PF3D7_1103400	Pf3D7_11_v3	146427	+	4389	1.198	-0.028	2.425	3.263	3.343	1.93e-03	5.78e-02	-1.310	FeS cluster assembly protein SufD, putative	SufD
42	PF3D7_0405400	Pf3D7_04_v3	291251	+	9726	-0.562	-1.533	0.410	10.748	-3.333	1.97e-03	5.87e-02	-1.665	pre-mRNA-processing-splicing factor 8, putative	PRPF8
56	PF3D7_0421300	Pf3D7_04_v3	969031	-	7561	-1.056	-1.582	-0.531	4.877	-3.320	2.05e-03	5.87e-02	-1.447	erythrocyte membrane protein 1, PfEMP1	VAR
247	PF3D7_1226600	Pf3D7_12_v3	1077868	-	909	1.498	0.096	2.900	-0.283	3.319	2.05e-03	5.87e-02	-1.406	proliferating cell nuclear antigen 2	PCNA2
255	PF3D7_1234500	Pf3D7_12_v3	1439896	-	1155	0.626	0.114	1.138	4.918	3.325	2.02e-03	5.87e-02	-1.435	conserved Plasmodium protein, unknown function	NA
308	PF3D7_1364000	Pf3D7_13_v3	2564625	+	2484	0.987	0.420	1.554	3.797	3.328	2.01e-03	5.87e-02	-1.369	conserved Plasmodium protein, unknown function	NA
313	PF3D7_1372100	Pf3D7_13_v3	2837053	+	2006	3.129	2.299	3.958	1.578	3.365	2.06e-03	5.87e-02	-1.336	Plasmodium exported protein (PHISTb), unknown function	GEXP04
339	PF3D7_1445800	Pf3D7_14_v3	1878658	-	3920	1.067	0.776	1.358	1.539	3.321	2.05e-03	5.87e-02	-1.355	conserved Plasmodium membrane protein, unknown function	NA
280	PF3D7_1307700	Pf3D7_13_v3	344525	+	3708	0.582	-0.368	1.531	6.383	3.313	2.09e-03	5.94e-02	-1.581	conserved Plasmodium protein, unknown function	NA
109	PF3D7_0703400	Pf3D7_07_v3	129370	-	2463	1.161	0.838	1.484	3.395	3.307	2.12e-03	5.99e-02	-1.406	conserved Plasmodium protein, unknown function	NA
183	PF3D7_1016100	Pf3D7_10_v3	643558	-	774	1.160	0.663	1.658	0.683	3.303	2.15e-03	6.01e-02	-1.409	conserved Plasmodium protein, unknown function	NA
358	PF3D7_1477700	Pf3D7_14_v3	3202931	+	1087	2.091	1.317	2.865	1.770	3.316	2.17e-03	6.04e-02	-1.395	Plasmodium exported protein (PHISTa), unknown function	Pfg14-748
64	PF3D7_0508700	Pf3D7_05_v3	358261	+	4473	-0.499	-1.326	0.327	7.639	-3.287	2.24e-03	6.05e-02	-1.721	pre-mRNA-processing ATP-dependent RNA helicase PRP5, putative	PRP5
144	PF3D7_0814100	Pf3D7_08_v3	682518	-	1055	0.938	-0.783	2.659	4.348	3.287	2.24e-03	6.05e-02	-1.492	conserved Plasmodium protein, unknown function	NA
178	PF3D7_1009300	Pf3D7_10_v3	377906	-	1803	1.211	0.885	1.536	3.019	3.287	2.24e-03	6.05e-02	-1.441	conserved Plasmodium protein, unknown function	NA
295	PF3D7_1344200	Pf3D7_13_v3	1769129	+	2799	-0.564	-1.236	0.108	9.434	-3.286	2.25e-03	6.05e-02	-1.777	heat shock protein 110, putative	HSP110
330	PF3D7_1427200	Pf3D7_14_v3	1061805	+	975	-1.619	-2.155	-1.082	1.505	-3.289	2.25e-03	6.05e-02	-1.430	selenoprotein	Sel4
44	PF3D7_0412400	Pf3D7_04_v3	545987	-	7824	-0.919	-1.577	-0.261	3.465	-3.283	2.27e-03	6.06e-02	-1.458	erythrocyte membrane protein 1, PfEMP1	VAR
32	PF3D7_0317100	Pf3D7_03_v3	686282	+	3201	0.874	0.596	1.152	2.504	3.274	2.33e-03	6.06e-02	-1.464	6-cysteine protein	B9
82	PF3D7_0531000	Pf3D7_05_v3	1267410	+	2130	0.713	-0.601	2.027	4.964	3.276	2.31e-03	6.06e-02	-1.559	conserved Plasmodium protein, unknown function	NA
134	PF3D7_0800300	Pf3D7_08_v3	40948	+	9992	-1.073	-1.392	-0.753	5.027	-3.282	2.29e-03	6.06e-02	-1.553	erythrocyte membrane protein 1, PfEMP1	VAR
289	PF3D7_1321700	Pf3D7_13_v3	902383	+	2784	-0.538	-0.896	-0.181	9.122	-3.276	2.31e-03	6.06e-02	-1.799	splicing factor 1	SF1
273	PF3D7_1302700	Pf3D7_13_v3	145174	+	5025	-0.474	-1.190	0.241	8.882	-3.270	2.35e-03	6.09e-02	-1.808	ATP-dependent RNA helicase DHR1, putative	NA
169	PF3D7_0926500	Pf3D7_09_v3	1075915	-	5769	1.173	0.733	1.614	0.469	3.256	2.44e-03	6.26e-02	-1.518	conserved Plasmodium protein, unknown function	NA
221	PF3D7_1128100	Pf3D7_11_v3	1094909	-	1023	-0.703	-1.004	-0.402	5.252	-3.253	2.46e-03	6.26e-02	-1.636	prefoldin subunit 5, putative	NA
233	PF3D7_1205700	Pf3D7_12_v3	253155	+	969	1.229	0.775	1.684	0.855	3.254	2.45e-03	6.26e-02	-1.515	targeted glyoxalase II	tGloII
17	PF3D7_0209700	Pf3D7_02_v3	400153	-	1707	0.555	-0.119	1.228	8.789	3.232	2.61e-03	6.32e-02	-1.899	RING zinc finger protein, putative	NA
22	PF3D7_0220500	Pf3D7_02_v3	823825	-	1040	-0.875	-2.077	0.327	6.458	-3.238	2.57e-03	6.32e-02	-1.757	Plasmodium exported protein (hyp2), unknown function	NA
87	PF3D7_0606800	Pf3D7_06_v3	288377	-	900	1.551	1.311	1.791	3.382	3.241	2.60e-03	6.32e-02	-1.573	probable protein, unknown function	NA
130	PF3D7_0723900	Pf3D7_07_v3	1000701	-	4046	-0.612	-0.899	-0.325	7.826	-3.238	2.57e-03	6.32e-02	-1.851	RNA-binding protein, putative	NA
187	PF3D7_1021900	Pf3D7_10_v3	905473	-	6873	-0.993	-1.349	-0.638	6.736	-3.246	2.57e-03	6.32e-02	-1.784	PHAX domain-containing protein, putative	NA
199	PF3D7_1100300	Pf3D7_11_v3	45056	+	1178	1.993	1.575	2.412	-0.537	3.236	2.60e-03	6.32e-02	-1.598	rifin	RIF
241	PF3D7_1217000	Pf3D7_12_v3	674349	-	429	1.119	0.313	1.924	1.672	3.236	2.58e-03	6.32e-02	-1.546	conserved Plasmodium protein, unknown function	NA
317	PF3D7_1401600	Pf3D7_14_v3	61364	-	1625	-0.760	-1.042	-0.478	8.852	-3.236	2.61e-03	6.32e-02	-1.901	Plasmodium exported protein (PHISTb), unknown function	NA
70	PF3D7_0518300	Pf3D7_05_v3	759831	-	1168	-0.484	-0.912	-0.056	6.571	-3.226	2.65e-03	6.33e-02	-1.809	proteasome subunit beta type-1, putative	NA
72	PF3D7_0521000	Pf3D7_05_v3	859373	-	1691	-0.687	-1.390	0.017	5.971	-3.225	2.66e-03	6.33e-02	-1.762	conserved Plasmodium protein, unknown function	NA
98	PF3D7_0621500	Pf3D7_06_v3	881963	+	1032	1.065	0.072	2.058	1.161	3.225	2.65e-03	6.33e-02	-1.574	ribonuclease P/MRP protein subunit RPP1, putative	RPP1
174	PF3D7_0936800	Pf3D7_09_v3	1458392	+	1471	-0.876	-1.190	-0.562	10.878	-3.220	2.77e-03	6.48e-02	-1.957	Plasmodium exported protein (PHISTc), unknown function	NA
181	PF3D7_1013000	Pf3D7_10_v3	500210	+	2012	1.140	0.529	1.751	2.844	3.208	2.78e-03	6.48e-02	-1.624	zinc finger protein, putative	NA
184	PF3D7_1016200	Pf3D7_10_v3	646054	+	1683	1.055	0.321	1.789	4.570	3.206	2.80e-03	6.48e-02	-1.710	Rab3 GTPase-activating protein non-catalytic subunit, putative	NA
227	PF3D7_1140800	Pf3D7_11_v3	1633920	+	2412	0.505	-0.045	1.055	6.676	3.212	2.75e-03	6.48e-02	-1.849	conserved Plasmodium protein, unknown function	NA
230	PF3D7_1149500	Pf3D7_11_v3	1991359	-	2660	-0.653	-1.498	0.192	8.007	-3.204	2.81e-03	6.48e-02	-1.927	ring-infected erythrocyte surface antigen 2, pseudogene	RESA2
319	PF3D7_1410500	Pf3D7_14_v3	423751	-	500	1.042	0.705	1.378	1.400	3.205	2.80e-03	6.48e-02	-1.618	conserved Plasmodium protein, unknown function	NA
104	PF3D7_0631600	Pf3D7_06_v3	1323294	+	1142	-1.234	-1.641	-0.828	2.559	-3.201	2.83e-03	6.49e-02	-1.631	exported protein family 4	EPF4
323	PF3D7_1414500	Pf3D7_14_v3	578369	-	9161	-0.636	-0.920	-0.351	7.984	-3.197	2.86e-03	6.52e-02	-1.965	atypical protein kinase, ABC-1 family, putative	ABCk2
12	PF3D7_0201800	Pf3D7_02_v3	86832	-	1960	-0.527	-0.803	-0.252	9.437	-3.178	3.02e-03	6.61e-02	-2.046	knob associated heat shock protein 40	KAHsp40
33	PF3D7_0317500	Pf3D7_03_v3	716523	-	5309	0.587	-0.080	1.253	7.115	3.180	3.00e-03	6.61e-02	-1.961	kinesin-5	EG5
52	PF3D7_0418300	Pf3D7_04_v3	819362	-	2979	0.610	0.114	1.106	10.470	3.186	2.95e-03	6.61e-02	-2.036	conserved Plasmodium protein, unknown function	NA
67	PF3D7_0511000	Pf3D7_05_v3	467585	-	516	-0.538	-0.738	-0.337	8.120	-3.185	2.96e-03	6.61e-02	-1.988	translationally-controlled tumor protein homolog	TCTP
263	PF3D7_1244300	Pf3D7_12_v3	1857849	+	242	-1.945	-2.961	-0.930	2.568	-3.199	2.97e-03	6.61e-02	-1.662	ACEA small nucleolar RNA U3	NA
277	PF3D7_1304300	Pf3D7_13_v3	231083	+	642	1.477	0.660	2.294	0.552	3.180	3.00e-03	6.61e-02	-1.683	conserved Plasmodium protein, unknown function	NA
278	PF3D7_1305400	Pf3D7_13_v3	268785	-	1953	0.561	0.218	0.904	5.309	3.182	2.98e-03	6.61e-02	-1.821	AAR2 protein, putative	NA
34	PF3D7_0319600	Pf3D7_03_v3	817913	+	783	-0.442	-0.957	0.073	8.336	-3.170	3.08e-03	6.72e-02	-2.045	elongation factor 1 (EF-1), putative	NA
195	PF3D7_1035800	Pf3D7_10_v3	1420533	+	2139	-1.293	-1.677	-0.909	9.469	-3.201	3.10e-03	6.72e-02	-2.007	probable protein, unknown function	M712
283	PF3D7_1309400	Pf3D7_13_v3	431892	+	3984	-0.750	-1.414	-0.086	5.757	-3.166	3.12e-03	6.72e-02	-1.885	HORMA domain protein, putative	NA
173	PF3D7_0935900	Pf3D7_09_v3	1420483	-	2325	-0.762	-1.083	-0.440	13.744	-3.169	3.13e-03	6.73e-02	-2.072	ring-exported protein 1	REX1
152	PF3D7_0829100	Pf3D7_08_v3	1252349	+	1448	-0.521	-1.286	0.244	7.060	-3.160	3.16e-03	6.75e-02	-2.006	conserved protein, unknown function	NA
222	PF3D7_1133000	Pf3D7_11_v3	1275574	+	90	1.310	0.942	1.678	0.955	3.158	3.18e-03	6.77e-02	-1.727	conserved Plasmodium protein, unknown function	NA
16	PF3D7_0205400	Pf3D7_02_v3	223478	+	1374	0.446	0.105	0.787	6.179	3.149	3.26e-03	6.80e-02	-1.969	PCI domain-containing protein, putative	NA
55	PF3D7_0420000	Pf3D7_04_v3	894612	-	10113	-0.524	-1.375	0.327	9.311	-3.146	3.29e-03	6.80e-02	-2.125	zinc finger protein, putative	NA
182	PF3D7_1015800	Pf3D7_10_v3	633682	+	1605	1.197	0.525	1.870	0.318	3.151	3.24e-03	6.80e-02	-1.749	ribonucleoside-diphosphate reductase small chain, putative	NA
258	PF3D7_1240400	Pf3D7_12_v3	1704512	+	7979	-0.936	-1.157	-0.715	4.827	-3.148	3.27e-03	6.80e-02	-1.857	erythrocyte membrane protein 1, PfEMP1	VAR
355	PF3D7_1468100	Pf3D7_14_v3	2786308	-	8016	-0.558	-0.954	-0.161	10.206	-3.146	3.28e-03	6.80e-02	-2.133	conserved Plasmodium protein, unknown function	NA
357	PF3D7_1472300	Pf3D7_14_v3	2954108	+	3001	1.050	0.167	1.932	4.451	3.145	3.30e-03	6.80e-02	-1.843	conserved Plasmodium membrane protein, unknown function	NA
66	PF3D7_0509800	Pf3D7_05_v3	410268	+	5041	-0.385	-0.757	-0.013	8.254	-3.141	3.33e-03	6.80e-02	-2.114	phosphatidylinositol 4-kinase	PI4K
232	PF3D7_1200200	Pf3D7_12_v3	26321	-	1367	-1.845	-2.273	-1.417	-0.252	-3.141	3.33e-03	6.80e-02	-1.797	rifin	RIF
226	PF3D7_1140200	Pf3D7_11_v3	1601257	-	1822	-1.160	-1.579	-0.742	3.820	-3.140	3.35e-03	6.81e-02	-1.826	conserved Plasmodium protein, unknown function	NA
348	PF3D7_1457100	Pf3D7_14_v3	2340784	+	2244	-0.895	-1.549	-0.240	6.629	-3.139	3.39e-03	6.85e-02	-2.013	conserved Plasmodium protein, unknown function	NA
200	PF3D7_1102600	Pf3D7_11_v3	123818	-	919	1.461	0.883	2.039	2.317	3.132	3.43e-03	6.91e-02	-1.791	Plasmodium exported protein, unknown function	GEXP14
112	PF3D7_0705600	Pf3D7_07_v3	281035	-	3399	0.833	0.363	1.303	3.988	3.125	3.48e-03	6.96e-02	-1.857	RNA helicase, putative	NA
352	PF3D7_1460500	Pf3D7_14_v3	2466091	+	4899	1.016	0.429	1.604	2.431	3.123	3.49e-03	6.96e-02	-1.807	conserved Plasmodium protein, unknown function	NA
3	PF3D7_0101000	Pf3D7_01_v3	65817	-	1173	-2.246	-2.928	-1.565	-1.073	-3.119	3.57e-03	7.06e-02	-1.882	rifin	RIF
90	PF3D7_0609700	Pf3D7_06_v3	413652	+	6130	-0.563	-1.557	0.430	9.552	-3.111	3.61e-03	7.06e-02	-2.211	conserved Plasmodium protein, unknown function	NA
186	PF3D7_1019300	Pf3D7_10_v3	774929	-	5559	0.842	0.580	1.103	4.369	3.114	3.58e-03	7.06e-02	-1.903	zinc finger protein, putative	NA
272	PF3D7_1301400	Pf3D7_13_v3	82718	+	1301	-0.891	-1.162	-0.619	8.053	-3.118	3.61e-03	7.06e-02	-2.129	Plasmodium exported protein (hyp12), unknown function	HYP12
165	PF3D7_0915500	Pf3D7_09_v3	657418	+	1995	1.320	0.789	1.851	0.044	3.109	3.63e-03	7.07e-02	-1.847	conserved Plasmodium protein, unknown function	NA
123	PF3D7_0713500	Pf3D7_07_v3	614385	+	2865	0.925	0.534	1.316	4.314	3.100	3.72e-03	7.07e-02	-1.938	conserved Plasmodium protein, unknown function	NA
141	PF3D7_0808700	Pf3D7_08_v3	440408	+	7655	-0.981	-1.345	-0.618	4.547	-3.102	3.69e-03	7.07e-02	-1.952	erythrocyte membrane protein 1, PfEMP1	VAR
145	PF3D7_0817100	Pf3D7_08_v3	774299	+	2493	1.043	0.215	1.870	0.070	3.101	3.70e-03	7.07e-02	-1.864	tRNA modification GTPase, putative	NA
162	PF3D7_0913100	Pf3D7_09_v3	571031	-	2319	1.169	0.432	1.905	-0.164	3.102	3.69e-03	7.07e-02	-1.865	conserved Plasmodium protein, unknown function	NA
345	PF3D7_1451100	Pf3D7_14_v3	2090902	+	2499	-0.648	-1.295	-0.001	12.559	-3.105	3.67e-03	7.07e-02	-2.231	elongation factor 2	eEF2
281	PF3D7_1308300	Pf3D7_13_v3	372260	+	387	0.444	-0.083	0.971	7.958	3.092	3.80e-03	7.19e-02	-2.222	40S ribosomal protein S27	RPS27
27	PF3D7_0304900	Pf3D7_03_v3	231793	-	513	0.801	0.116	1.486	5.085	3.080	3.92e-03	7.22e-02	-2.035	conserved Plasmodium protein, unknown function	NA
76	PF3D7_0524800	Pf3D7_05_v3	1021408	-	2900	0.882	0.028	1.736	3.247	3.087	3.84e-03	7.22e-02	-1.915	ubiquitin fusion degradation protein 1, putative	UFD1
225	PF3D7_1137300	Pf3D7_11_v3	1466197	-	2070	0.450	-0.267	1.166	7.350	3.080	3.92e-03	7.22e-02	-2.218	CLPTM1 domain-containing protein, putative	NA
252	PF3D7_1231600	Pf3D7_12_v3	1301098	-	3507	-0.706	-1.747	0.336	6.288	-3.084	3.88e-03	7.22e-02	-2.140	pre-mRNA-splicing factor ATP-dependent RNA helicase PRP2, putative	PRP2
282	PF3D7_1309100	Pf3D7_13_v3	418820	+	1302	-0.722	-1.280	-0.165	8.832	-3.088	3.87e-03	7.22e-02	-2.267	60S ribosomal protein L24, putative	NA
291	PF3D7_1324200	Pf3D7_13_v3	1000100	-	1783	-0.797	-1.141	-0.454	7.145	-3.086	3.89e-03	7.22e-02	-2.192	micro-fibrillar-associated protein, putative	NA
119	PF3D7_0712300	Pf3D7_07_v3	542906	-	7615	-1.223	-2.264	-0.181	3.752	-3.079	3.97e-03	7.25e-02	-1.970	erythrocyte membrane protein 1, PfEMP1	VAR
307	PF3D7_1362300	Pf3D7_13_v3	2493143	+	570	0.782	-0.312	1.876	3.668	3.075	3.97e-03	7.25e-02	-1.960	conserved protein, unknown function	NA
240	PF3D7_1215900	Pf3D7_12_v3	641552	+	1968	0.743	0.298	1.187	4.806	3.068	4.04e-03	7.35e-02	-2.053	serpentine receptor, putative	SR10
20	PF3D7_0216400	Pf3D7_02_v3	675431	+	2169	0.789	0.122	1.457	0.530	3.064	4.09e-03	7.37e-02	-1.935	vacuolar protein sorting-associated protein 45, putative	VPS45
172	PF3D7_0932900	Pf3D7_09_v3	1309467	-	477	0.939	0.530	1.349	2.103	3.065	4.08e-03	7.37e-02	-1.934	conserved Plasmodium protein, unknown function	NA
292	PF3D7_1326700	Pf3D7_13_v3	1125280	+	1629	1.336	0.904	1.768	3.634	3.063	4.16e-03	7.46e-02	-1.997	conserved Apicomplexan protein, unknown function	NA
160	PF3D7_0907900	Pf3D7_09_v3	367865	-	925	-1.480	-2.225	-0.735	3.656	-3.067	4.19e-03	7.48e-02	-2.006	peptide deformylase	PDF
333	PF3D7_1434300	Pf3D7_14_v3	1372903	+	1695	-0.408	-1.424	0.608	8.746	-3.050	4.25e-03	7.55e-02	-2.352	Hsp70/Hsp90 organizing protein	HOP
353	PF3D7_1462800	Pf3D7_14_v3	2559098	+	1250	-0.693	-1.932	0.546	13.081	-3.050	4.27e-03	7.56e-02	-2.364	glyceraldehyde-3-phosphate dehydrogenase	GAPDH
5	PF3D7_0108500	Pf3D7_01_v3	349170	+	540	-0.875	-2.335	0.586	10.163	-3.051	4.39e-03	7.58e-02	-2.381	conserved Plasmodium protein, unknown function	NA
10	PF3D7_0200100	Pf3D7_02_v3	25232	+	5937	-1.299	-2.059	-0.540	3.963	-3.049	4.33e-03	7.58e-02	-2.044	erythrocyte membrane protein 1, PfEMP1	VAR
214	PF3D7_1122300	Pf3D7_11_v3	846929	+	1086	0.944	0.421	1.466	3.809	3.043	4.32e-03	7.58e-02	-2.047	conserved Plasmodium protein, unknown function	NA
215	PF3D7_1122900	Pf3D7_11_v3	878969	+	16305	-1.086	-1.508	-0.664	1.411	-3.039	4.37e-03	7.58e-02	-1.988	dynein heavy chain, putative	NA
254	PF3D7_1233100	Pf3D7_12_v3	1359169	+	408	-0.794	-1.469	-0.119	4.068	-3.041	4.35e-03	7.58e-02	-2.051	conserved protein, unknown function	NA
270	PF3D7_1253100	Pf3D7_12_v3	2171342	+	1008	0.614	0.151	1.077	6.992	3.039	4.37e-03	7.58e-02	-2.295	Plasmodium exported protein (PHISTa), unknown function	NA
115	PF3D7_0709600	Pf3D7_07_v3	429857	-	3902	-0.489	-0.848	-0.129	7.337	-3.035	4.41e-03	7.59e-02	-2.325	ribonucleases P/MRP protein subunit POP1, putative	POP1
223	PF3D7_1133700	Pf3D7_11_v3	1302173	+	3815	-0.680	-1.110	-0.249	10.033	-3.034	4.46e-03	7.60e-02	-2.412	FHA domain-containing protein, putative	NA
264	PF3D7_1244800	Pf3D7_12_v3	1873194	-	2094	-0.452	-2.303	1.399	7.567	-3.030	4.48e-03	7.60e-02	-2.356	cytoplasmic translation machinery associated protein, putative	NA
269	PF3D7_1251400	Pf3D7_12_v3	2097436	-	1410	1.035	0.691	1.379	1.657	3.031	4.46e-03	7.60e-02	-2.004	conserved Plasmodium protein, unknown function	NA
48	PF3D7_0415300	Pf3D7_04_v3	681810	+	4159	-0.547	-0.925	-0.169	8.627	-3.020	4.59e-03	7.68e-02	-2.419	cdc2-related protein kinase 3	CRK3
108	PF3D7_0703200	Pf3D7_07_v3	122513	-	4623	-0.955	-1.527	-0.383	4.508	-3.017	4.63e-03	7.68e-02	-2.153	conserved Plasmodium protein, unknown function	NA
118	PF3D7_0712000	Pf3D7_07_v3	527338	-	7794	-1.572	-1.966	-1.178	3.236	-3.029	4.61e-03	7.68e-02	-2.059	erythrocyte membrane protein 1, PfEMP1	VAR
155	PF3D7_0833500	Pf3D7_08_v3	1435794	-	7656	-0.978	-1.408	-0.547	4.340	-3.022	4.57e-03	7.68e-02	-2.123	erythrocyte membrane protein 1, PfEMP1	VAR
188	PF3D7_1023000	Pf3D7_10_v3	961066	-	1242	0.838	0.065	1.610	1.337	3.016	4.65e-03	7.68e-02	-2.035	conserved Plasmodium membrane protein, unknown function	NA
300	PF3D7_1347500	Pf3D7_13_v3	1897983	-	1380	-0.472	-0.748	-0.196	12.054	-3.015	4.65e-03	7.68e-02	-2.454	DNA/RNA-binding protein Alba 4	ALBA4
318	PF3D7_1404900	Pf3D7_14_v3	170000	+	894	0.405	-0.046	0.855	8.338	3.020	4.59e-03	7.68e-02	-2.410	conserved Plasmodium protein, unknown function	NA
92	PF3D7_0613600	Pf3D7_06_v3	554457	+	3772	1.236	0.284	2.188	0.053	3.009	4.73e-03	7.71e-02	-2.056	conserved Plasmodium protein, unknown function	NA
125	PF3D7_0716000	Pf3D7_07_v3	703207	+	3378	-0.490	-0.849	-0.130	8.568	-3.008	4.74e-03	7.71e-02	-2.448	RNA-binding protein, putative	NA
167	PF3D7_0923100	Pf3D7_09_v3	941830	-	669	1.113	0.506	1.720	1.302	3.009	4.73e-03	7.71e-02	-2.049	OTU domain-containing protein, putative	NA
239	PF3D7_1214600	Pf3D7_12_v3	613561	-	1014	-0.563	-1.043	-0.084	4.766	-3.012	4.70e-03	7.71e-02	-2.178	adrenodoxin-type ferredoxin, putative	NA
100	PF3D7_0625400	Pf3D7_06_v3	1032536	-	1239	0.554	-0.780	1.888	7.778	3.005	4.77e-03	7.73e-02	-2.416	conserved Plasmodium protein, unknown function	NA
79	PF3D7_0528100	Pf3D7_05_v3	1157840	-	3714	-0.377	-1.096	0.342	9.370	-2.997	4.88e-03	7.81e-02	-2.490	AP-1 complex subunit beta, putative	NA
191	PF3D7_1025500	Pf3D7_10_v3	1067652	-	19341	-1.108	-1.901	-0.316	0.450	-2.998	4.86e-03	7.81e-02	-2.074	conserved Plasmodium protein, unknown function	NA
194	PF3D7_1030100	Pf3D7_10_v3	1224519	-	4574	-0.406	-1.677	0.865	8.759	-2.997	4.88e-03	7.81e-02	-2.478	pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22, putative	PRP22
77	PF3D7_0527500	Pf3D7_05_v3	1143618	+	1742	-0.398	-1.848	1.052	9.586	-2.992	4.94e-03	7.83e-02	-2.505	Hsc70-interacting protein	HIP
131	PF3D7_0724000	Pf3D7_07_v3	1006335	+	5811	0.875	0.418	1.332	2.241	2.994	4.92e-03	7.83e-02	-2.094	Rab GTPase activator and protein kinase, putative	NA
268	PF3D7_1250800	Pf3D7_12_v3	2077718	+	5170	-0.475	-0.773	-0.177	6.852	-2.991	4.95e-03	7.83e-02	-2.402	DNA repair protein rhp16, putative	NA
340	PF3D7_1446300	Pf3D7_14_v3	1898351	+	3576	1.129	0.535	1.724	4.066	2.990	5.01e-03	7.90e-02	-2.191	conserved Plasmodium membrane protein, unknown function	NA
179	PF3D7_1011800	Pf3D7_10_v3	455398	+	3420	-0.579	-1.305	0.146	10.624	-2.984	5.04e-03	7.92e-02	-2.531	PRE-binding protein	PREBP
274	PF3D7_1302900	Pf3D7_13_v3	154992	+	2403	1.025	0.147	1.903	3.537	2.980	5.10e-03	7.98e-02	-2.176	conserved Plasmodium protein, unknown function	NA
235	PF3D7_1208600	Pf3D7_12_v3	402300	+	228	-0.700	-1.229	-0.171	3.757	-2.977	5.15e-03	8.00e-02	-2.206	mitochondrial import inner membrane translocase subunit TIM10, putative	TIM10
284	PF3D7_1309600	Pf3D7_13_v3	438510	+	867	0.727	0.325	1.129	4.309	2.976	5.15e-03	8.00e-02	-2.227	ribosomal RNA methyltransferase, putative	NA
11	PF3D7_0201600	Pf3D7_02_v3	77251	-	1558	-0.649	-1.469	0.172	9.150	-2.971	5.23e-03	8.01e-02	-2.534	PHISTb domain-containing RESA-like protein 1	RLP1
18	PF3D7_0211800	Pf3D7_02_v3	475242	+	1833	-0.643	-1.218	-0.068	9.283	-2.961	5.37e-03	8.01e-02	-2.576	asparagine–tRNA ligase	AsnRS
97	PF3D7_0621300	Pf3D7_06_v3	873809	+	2382	0.443	-0.422	1.307	7.592	2.960	5.37e-03	8.01e-02	-2.519	mRNA binding Pumilio-homology domain protein, putative	NA
129	PF3D7_0719900	Pf3D7_07_v3	865927	+	10206	-0.417	-1.081	0.248	7.724	-2.959	5.39e-03	8.01e-02	-2.534	conserved Plasmodium membrane protein, unknown function	NA
135	PF3D7_0801700	Pf3D7_08_v3	112299	+	5579	-0.589	-0.932	-0.246	6.129	-2.966	5.29e-03	8.01e-02	-2.408	sentrin-specific protease 2, putative	SENP2
137	PF3D7_0804700	Pf3D7_08_v3	271417	-	5997	-0.573	-1.463	0.317	5.755	-2.962	5.34e-03	8.01e-02	-2.382	conserved Plasmodium protein, unknown function	NA
159	PF3D7_0907700	Pf3D7_09_v3	364069	-	840	0.415	0.186	0.645	7.929	2.970	5.23e-03	8.01e-02	-2.513	subunit of proteaseome activator complex, putative	PA28
217	PF3D7_1124100	Pf3D7_11_v3	951382	-	4962	-0.411	-0.946	0.123	8.014	-2.963	5.34e-03	8.01e-02	-2.538	beige/BEACH domain protein, putative	NA
256	PF3D7_1235300	Pf3D7_12_v3	1470713	+	4989	-0.568	-1.359	0.222	9.292	-2.966	5.29e-03	8.01e-02	-2.560	CCR4-NOT transcription complex subunit 4, putative	NOT4
301	PF3D7_1350100	Pf3D7_13_v3	2005962	-	1989	-0.430	-1.427	0.567	9.206	-2.962	5.34e-03	8.01e-02	-2.572	lysine–tRNA ligase	KRS1
312	PF3D7_1366500	Pf3D7_13_v3	2661573	+	450	1.090	0.675	1.506	0.730	2.968	5.26e-03	8.01e-02	-2.136	nucleoside diphosphate kinase	NDK
350	PF3D7_1458000	Pf3D7_14_v3	2387786	+	1710	0.339	-0.118	0.796	8.196	2.974	5.19e-03	8.01e-02	-2.513	cysteine proteinase falcipain 1	FP1
61	PF3D7_0502500	Pf3D7_05_v3	114149	+	1785	1.611	0.861	2.360	0.201	2.957	5.42e-03	8.02e-02	-2.162	conserved Plasmodium protein, unknown function	NA
354	PF3D7_1466300	Pf3D7_14_v3	2709418	+	3775	-0.392	-1.138	0.353	9.366	-2.954	5.46e-03	8.05e-02	-2.594	26S proteasome regulatory subunit RPN2, putative	RPN2
151	PF3D7_0826900	Pf3D7_08_v3	1164655	+	2551	0.987	0.185	1.788	3.078	2.949	5.54e-03	8.14e-02	-2.215	conserved Plasmodium protein, unknown function	NA
80	PF3D7_0528800	Pf3D7_05_v3	1180425	-	1614	0.476	-0.329	1.281	6.073	2.942	5.64e-03	8.23e-02	-2.454	nucleolar preribosomal GTPase, putative	NA
257	PF3D7_1239800	Pf3D7_12_v3	1660451	+	17304	-1.106	-1.531	-0.682	3.686	-2.944	5.62e-03	8.23e-02	-2.275	conserved Plasmodium protein, unknown function	NA
39	PF3D7_0404300	Pf3D7_04_v3	234014	-	3000	-0.853	-1.708	0.001	7.533	-2.947	5.68e-03	8.23e-02	-2.559	conserved Plasmodium protein, unknown function	NA
185	PF3D7_1019100	Pf3D7_10_v3	766168	-	5787	-1.392	-1.726	-1.058	0.749	-2.939	5.67e-03	8.23e-02	-2.197	conserved Plasmodium protein, unknown function	NA
304	PF3D7_1355200	Pf3D7_13_v3	2191058	-	3054	1.630	0.890	2.370	0.536	2.939	5.71e-03	8.24e-02	-2.201	RAP protein, putative	NA
328	PF3D7_1424500	Pf3D7_14_v3	979464	+	142	-0.825	-1.714	0.063	3.590	-2.929	5.82e-03	8.37e-02	-2.272	small nucleolar RNA snoR27	NA
293	PF3D7_1338600	Pf3D7_13_v3	1556659	-	3076	1.267	0.697	1.837	0.039	2.928	5.85e-03	8.39e-02	-2.223	conserved Plasmodium protein, unknown function	NA
311	PF3D7_1366000	Pf3D7_13_v3	2635213	+	276	1.117	0.785	1.450	2.202	2.924	5.91e-03	8.45e-02	-2.247	conserved Plasmodium protein, unknown function	NA
236	PF3D7_1210300	Pf3D7_12_v3	465115	+	630	0.713	-0.071	1.498	3.554	2.919	5.97e-03	8.51e-02	-2.309	conserved Plasmodium protein, unknown function	NA
249	PF3D7_1228900	Pf3D7_12_v3	1180670	-	4814	-0.607	-1.072	-0.142	6.434	-2.916	6.03e-03	8.56e-02	-2.550	conserved Plasmodium protein, unknown function	NA
8	PF3D7_0115200	Pf3D7_01_v3	591849	+	1339	-2.053	-3.146	-0.961	-0.691	-2.917	6.08e-03	8.59e-02	-2.271	rifin	RIF
30	PF3D7_0311700	Pf3D7_03_v3	502698	+	3151	-1.459	-2.316	-0.601	0.983	-2.910	6.12e-03	8.59e-02	-2.258	plasmepsin VI	NA
46	PF3D7_0412900	Pf3D7_04_v3	576810	-	7859	-1.189	-1.516	-0.862	2.611	-2.911	6.10e-03	8.59e-02	-2.283	erythrocyte membrane protein 1, PfEMP1	VAR
43	PF3D7_0411900	Pf3D7_04_v3	528192	-	6294	-0.914	-1.287	-0.541	1.934	-2.905	6.20e-03	8.62e-02	-2.287	DNA polymerase alpha catalytic subunit A	NA
201	PF3D7_1102700	Pf3D7_11_v3	128789	+	276	-0.587	-0.982	-0.192	10.475	-2.905	6.20e-03	8.62e-02	-2.719	early transcribed membrane protein 11.1	ETRAMP11.1
279	PF3D7_1306400	Pf3D7_13_v3	297178	-	1182	-0.466	-1.327	0.396	7.247	-2.904	6.22e-03	8.62e-02	-2.626	26S protease regulatory subunit 10B, putative	RPT4
302	PF3D7_1353500	Pf3D7_13_v3	2144125	+	981	0.778	0.133	1.423	3.030	2.907	6.17e-03	8.62e-02	-2.313	RNA polymerase II transcription factor B subunit 4, putative	TFB4
2	mal_rna_17:rRNA	M76611	5577	-	195	-1.264	-1.671	-0.857	4.223	-2.903	6.33e-03	8.72e-02	-2.371	NA	NA
196	PF3D7_1037900	Pf3D7_10_v3	1502955	-	1368	1.025	0.342	1.708	2.136	2.897	6.34e-03	8.72e-02	-2.307	conserved Plasmodium protein, unknown function	NA
164	PF3D7_0915100	Pf3D7_09_v3	643232	-	812	-0.531	-1.152	0.090	6.543	-2.889	6.46e-03	8.87e-02	-2.619	SUMO-conjugating enzyme UBC9	UBC9
35	PF3D7_0323000	Pf3D7_03_v3	968675	-	528	-0.901	-1.197	-0.604	4.269	-2.885	6.53e-03	8.91e-02	-2.456	translation machinery-associated protein 7, putative	TMA7
309	PF3D7_1365000	Pf3D7_13_v3	2608698	+	1047	-0.839	-1.102	-0.577	3.815	-2.886	6.52e-03	8.91e-02	-2.386	conserved Plasmodium protein, unknown function	NA
60	PF3D7_0501400	Pf3D7_05_v3	74509	+	5334	-1.045	-1.303	-0.787	10.998	-2.901	6.65e-03	8.95e-02	-2.757	interspersed repeat antigen	FIRA
75	PF3D7_0523700	Pf3D7_05_v3	980754	-	4601	1.308	0.350	2.266	0.920	2.876	6.69e-03	8.95e-02	-2.331	conserved Plasmodium membrane protein, unknown function	NA
86	PF3D7_0601600	Pf3D7_06_v3	68833	-	861	1.227	-0.183	2.636	1.035	2.873	6.74e-03	8.95e-02	-2.337	tetratricopeptide repeat protein, putative	NA
93	PF3D7_0613900	Pf3D7_06_v3	579435	-	6462	1.190	-0.386	2.767	0.943	2.874	6.72e-03	8.95e-02	-2.334	myosin E, putative	myoE
96	PF3D7_0618200	Pf3D7_06_v3	764667	-	826	-0.533	-1.152	0.086	7.015	-2.871	6.78e-03	8.95e-02	-2.700	conserved Plasmodium protein, unknown function	NA
101	PF3D7_0625600	Pf3D7_06_v3	1039655	+	1896	0.840	-0.298	1.979	5.615	2.878	6.67e-03	8.95e-02	-2.563	poly(A) polymerase PAP, putative	NA
163	PF3D7_0913200	Pf3D7_09_v3	575679	+	831	-0.503	-1.221	0.215	8.866	-2.871	6.77e-03	8.95e-02	-2.781	elongation factor 1-beta	EF-1beta
228	PF3D7_1142400	Pf3D7_11_v3	1702089	-	1554	0.593	-0.547	1.732	5.970	2.878	6.64e-03	8.95e-02	-2.601	coproporphyrinogen-III oxidase	CPO
276	PF3D7_1303100	Pf3D7_13_v3	159024	+	892	-0.764	-1.043	-0.485	3.651	-2.879	6.62e-03	8.95e-02	-2.429	methyltransferase-like protein, putative	NA
334	PF3D7_1436500	Pf3D7_14_v3	1488706	+	1296	1.054	0.135	1.972	0.183	2.873	6.73e-03	8.95e-02	-2.335	GTP-binding protein, putative	NA
110	PF3D7_0703700	Pf3D7_07_v3	146645	-	750	0.495	-0.380	1.370	7.579	2.868	6.82e-03	8.98e-02	-2.733	conserved Plasmodium protein, unknown function	NA
171	PF3D7_0931400	Pf3D7_09_v3	1263347	+	1484	-0.845	-1.123	-0.567	3.547	-2.862	6.93e-03	9.00e-02	-2.430	conserved Plasmodium protein, unknown function	NA
206	PF3D7_1108600	Pf3D7_11_v3	369675	-	1032	-0.677	-1.052	-0.302	9.227	-2.866	6.92e-03	9.00e-02	-2.795	endoplasmic reticulum-resident calcium binding protein	ERC
306	PF3D7_1360100	Pf3D7_13_v3	2405249	-	969	-0.524	-0.778	-0.270	5.582	-2.864	6.88e-03	9.00e-02	-2.583	RNA-binding protein, putative	NA
329	PF3D7_1426000	Pf3D7_14_v3	1016133	-	486	0.490	0.116	0.864	8.627	2.863	6.90e-03	9.00e-02	-2.789	60S ribosomal protein L21	RPL21
15	PF3D7_0202500	Pf3D7_02_v3	127994	+	321	-0.663	-1.051	-0.275	12.139	-2.862	6.99e-03	9.04e-02	-2.822	early transcribed membrane protein 2	ETRAMP2
157	PF3D7_0903100	Pf3D7_09_v3	130140	-	798	0.695	0.070	1.319	4.700	2.858	7.00e-03	9.04e-02	-2.523	protein RER1, putative	RER1
21	PF3D7_0218700	Pf3D7_02_v3	763491	-	1701	-0.606	-1.170	-0.042	7.123	-2.852	7.11e-03	9.05e-02	-2.738	pre-mRNA-processing protein 45, putative	PRP45
150	PF3D7_0826100	Pf3D7_08_v3	1113369	-	25776	-0.526	-0.989	-0.064	10.275	-2.853	7.08e-03	9.05e-02	-2.840	E3 ubiquitin-protein ligase, putative	NA
192	PF3D7_1027300	Pf3D7_10_v3	1140589	-	2014	-0.763	-1.045	-0.481	8.469	-2.857	7.12e-03	9.05e-02	-2.799	peroxiredoxin	nPrx
250	PF3D7_1229600	Pf3D7_12_v3	1214043	-	3673	-1.015	-1.610	-0.421	1.452	-2.855	7.06e-03	9.05e-02	-2.378	conserved Plasmodium protein, unknown function	NA
266	PF3D7_1247400	Pf3D7_12_v3	1955124	-	915	-0.628	-1.393	0.137	6.237	-2.853	7.10e-03	9.05e-02	-2.676	peptidyl-prolyl cis-trans isomerase FKBP35	FKBP35
78	PF3D7_0528000	Pf3D7_05_v3	1156205	-	375	0.784	-1.169	2.738	3.675	2.849	7.17e-03	9.08e-02	-2.472	proteasome maturation factor UMP1, putative	UMP1
91	PF3D7_0612700	Pf3D7_06_v3	525987	-	1044	0.819	-0.189	1.826	1.993	2.847	7.20e-03	9.08e-02	-2.405	6-cysteine protein	P12
325	PF3D7_1417700	Pf3D7_14_v3	750330	+	1355	-0.593	-0.956	-0.231	4.828	-2.846	7.21e-03	9.08e-02	-2.565	conserved Plasmodium protein, unknown function	NA
49	PF3D7_0416000	Pf3D7_04_v3	701526	-	2637	-0.691	-1.273	-0.108	6.293	-2.845	7.24e-03	9.09e-02	-2.698	RNA-binding protein, putative	NA
26	PF3D7_0303400	Pf3D7_03_v3	178420	+	2708	1.000	0.628	1.372	1.354	2.833	7.46e-03	9.26e-02	-2.423	palmitoyltransferase DHHC1	DHHC1
158	PF3D7_0905300	Pf3D7_09_v3	251353	-	18357	-0.896	-1.244	-0.548	2.709	-2.834	7.44e-03	9.26e-02	-2.466	dynein heavy chain, putative	NA
208	PF3D7_1111000	Pf3D7_11_v3	434802	+	1740	0.564	-0.224	1.352	5.391	2.833	7.46e-03	9.26e-02	-2.644	tRNA m5C-methyltransferase, putative	NA
327	PF3D7_1423200	Pf3D7_14_v3	933059	+	2299	-0.588	-0.881	-0.294	5.853	-2.834	7.45e-03	9.26e-02	-2.693	peptidyl-prolyl cis-trans isomerase	CYP52
74	PF3D7_0523300	Pf3D7_05_v3	970266	-	697	1.001	0.197	1.805	0.700	2.826	7.59e-03	9.29e-02	-2.431	conserved Plasmodium protein, unknown function	NA
176	PF3D7_1002300	Pf3D7_10_v3	117242	+	1293	0.867	0.028	1.706	1.347	2.827	7.58e-03	9.29e-02	-2.437	conserved Plasmodium protein, unknown function	NA
290	PF3D7_1322100	Pf3D7_13_v3	920971	+	8479	-0.528	-1.188	0.132	9.385	-2.826	7.59e-03	9.29e-02	-2.884	histone-lysine N-methyltransferase SET2	SET2
294	PF3D7_1341100	Pf3D7_13_v3	1632602	-	108	-1.102	-1.788	-0.415	3.017	-2.826	7.60e-03	9.29e-02	-2.477	U6 spliceosomal RNA	NA
314	PF3D7_1373500	Pf3D7_13_v3	2884786	-	7555	-0.781	-1.245	-0.318	4.450	-2.826	7.60e-03	9.29e-02	-2.573	erythrocyte membrane protein 1, PfEMP1	VAR
245	PF3D7_1225200	Pf3D7_12_v3	1024455	-	3564	0.382	-0.352	1.116	6.893	2.824	7.64e-03	9.32e-02	-2.796	conserved Plasmodium protein, unknown function	NA
63	PF3D7_0506700	Pf3D7_05_v3	280886	+	2460	-0.562	-1.252	0.128	4.982	-2.815	7.81e-03	9.49e-02	-2.662	GTPase-activating protein, putative	NA
219	PF3D7_1126100	Pf3D7_11_v3	1018366	-	4130	0.858	0.339	1.377	1.600	2.811	7.90e-03	9.57e-02	-2.475	autophagy-related protein 7, putative	ATG7
88	PF3D7_0607000	Pf3D7_06_v3	293864	+	2934	-0.447	-1.635	0.742	10.481	-2.807	7.97e-03	9.61e-02	-2.949	translation initiation factor IF-2, putative	NA
94	PF3D7_0614200	Pf3D7_06_v3	593172	-	2733	0.813	-0.615	2.241	3.914	2.807	7.98e-03	9.61e-02	-2.582	cytosolic Fe-S cluster assembly factor NAR1, putative	NAR1
140	PF3D7_0808600	Pf3D7_08_v3	431165	+	7887	-0.842	-1.341	-0.344	4.353	-2.804	8.04e-03	9.66e-02	-2.623	erythrocyte membrane protein 1, PfEMP1	VAR
126	PF3D7_0717400	Pf3D7_07_v3	751877	+	2256	-0.411	-1.105	0.283	7.621	-2.802	8.08e-03	9.67e-02	-2.889	queuine tRNA-ribosyltransferase, putative	NA
332	PF3D7_1431600	Pf3D7_14_v3	1244018	+	1389	1.118	0.219	2.016	1.156	2.798	8.15e-03	9.74e-02	-2.493	succinyl-CoA ligase [ADP-forming] subunit beta, putative	NA
38	PF3D7_0400200	Pf3D7_04_v3	38955	+	1200	-1.094	-1.337	-0.852	2.992	-2.789	8.34e-03	9.86e-02	-2.562	erythrocyte membrane protein 1 (PfEMP1), exon 2, pseudogene	NA
89	PF3D7_0608700	Pf3D7_06_v3	358391	+	1813	-0.362	-0.916	0.193	9.108	-2.789	8.35e-03	9.86e-02	-2.977	T-complex protein 1 subunit zeta	CCT6
344	PF3D7_1450300	Pf3D7_14_v3	2056641	+	2598	0.766	0.095	1.436	5.175	2.789	8.35e-03	9.86e-02	-2.742	NADPH–cytochrome P450 reductase, putative	CPR
351	PF3D7_1459300	Pf3D7_14_v3	2432177	+	570	0.803	0.428	1.178	1.803	2.789	8.35e-03	9.86e-02	-2.529	OPA3-like protein, putative	NA
320	PF3D7_1412700	Pf3D7_14_v3	512363	+	3660	-0.569	-1.258	0.119	5.935	-2.787	8.40e-03	9.89e-02	-2.800	AAA family ATPase, putative	NA
113	PF3D7_0707900	Pf3D7_07_v3	366929	+	780	-0.414	-1.143	0.315	7.553	-2.784	8.46e-03	9.90e-02	-2.928	ribosomal protein S8e, putative	NA
261	PF3D7_1244100	Pf3D7_12_v3	1847677	+	4480	-0.482	-0.753	-0.210	5.912	-2.781	8.53e-03	9.90e-02	-2.816	N-alpha-acetyltransferase 15, NatA auxiliary subunit, putative	NA
321	PF3D7_1414100	Pf3D7_14_v3	560093	+	2232	0.548	-0.272	1.368	6.992	2.781	8.51e-03	9.90e-02	-2.898	conserved Plasmodium protein, unknown function	NA
336	PF3D7_1439100	Pf3D7_14_v3	1580750	+	8108	-0.574	-0.972	-0.177	6.512	-2.782	8.50e-03	9.90e-02	-2.863	DEAD/DEAH box helicase, putative	NA
342	PF3D7_1447200	Pf3D7_14_v3	1933985	+	1791	-0.429	-0.856	-0.001	7.819	-2.781	8.52e-03	9.90e-02	-2.951	conserved Plasmodium protein, unknown function	NA
253	PF3D7_1232200	Pf3D7_12_v3	1333134	+	1763	-0.941	-1.961	0.079	0.865	-2.777	8.60e-03	9.95e-02	-2.534	dihydrolipoyl dehydrogenase, mitochondrial	LPD1

Heatmap of deregulated genes

col_annot <- data.frame(row.names = colnames(v$E), stringsAsFactors = F)
col_annot$phenotype[substring(colnames(v$E), 1, 1) == "I"] <- "non-severe"
col_annot$phenotype[substring(colnames(v$E), 1, 1) == "S"] <- "severe"
col_annot$phenotype <- as.factor(col_annot$phenotype)

pheatmap(v2$E[rownames(v$E) %in% top_ring_ruv$GeneID, ], show_rownames = FALSE, scale = "row", annotation_col = col_annot, annotation_colors = list(phenotype = c(`non-severe` = colors[1], 
    severe = colors[2])))

Gene set analysis

First we can set up the gene sets after downloading the set annotations from PlasmoDB.

MIN_SET_SIZE <- 3

# GO sets
go.data <- fread("./data/PlasmoDB-35_Pfalciparum3D7_GO.gaf", skip = 1, sep = "\t", data.table = FALSE)
go.data <- go.data[go.data$V9 == "P", ]  #Looking at biological processes
go.terms <- unique(go.data$V5)
go.gene.sets <- lapply(go.terms, function(go) {
    unique(go.data$V2[grepl(go, go.data$V5, fixed = TRUE)])
})
names(go.gene.sets) <- go.terms
go.gene.sets <- go.gene.sets[unlist(lapply(go.gene.sets, length)) >= MIN_SET_SIZE]

# KEGG sets
kegg.annot.data <- fread("./data/KEGG_Metacyc_PlasmoDB.csv", data.table = FALSE)
kegg.annot.data <- kegg.annot.data[kegg.annot.data$`Pathway Source` == "KEGG", ]
kegg.gene.sets <- lapply(kegg.annot.data$Genes, function(x) unique(unlist(str_split(x, " \\| "))))
names(kegg.gene.sets) <- kegg.annot.data$`Pathway Id`
kegg.gene.sets <- kegg.gene.sets[unlist(lapply(kegg.gene.sets, length)) >= MIN_SET_SIZE]

Enrichment analysis

total.genes <- sum(grepl("^PF3D7", rownames(fc2$counts)))  #Size of universe
top_genes_set <- top_ring_ruv
go.test <- as.data.frame(do.call("rbind", lapply(go.gene.sets, function(gset) {
    set.size <- length(gset)
    gin_all <- gset[gset %in% top_genes_set$GeneID]
    gin_up <- gset[gset %in% top_genes_set$GeneID[top_genes_set$logFC > 0]]
    gin_down <- gset[gset %in% top_genes_set$GeneID[top_genes_set$logFC < 0]]
    result <- c(set.size = set.size, n.both = length(gin_all), n.up = length(gin_up), n.down = length(gin_down), p.value.both = phyper(length(gin_all) - 
        1, m = length(gset), n = total.genes - length(gset), k = nrow(top_genes_set), lower.tail = FALSE), p.value.up = phyper(length(gin_up) - 1, m = length(gset), 
        n = total.genes - length(gset), k = sum(top_genes_set$logFC > 0), lower.tail = FALSE), p.value.down = phyper(length(gin_down) - 1, m = length(gset), 
        n = total.genes - length(gset), k = sum(top_genes_set$logFC < 0), lower.tail = FALSE))
    return(result)
})))
go.test <- go.test[order(go.test$p.value.both), ]

go.test$p.value.both <- format(go.test$p.value.both, scientific = TRUE, digits = 3)
go.test$p.value.up <- format(go.test$p.value.up, scientific = TRUE, digits = 3)
go.test$p.value.down <- format(go.test$p.value.down, scientific = TRUE, digits = 3)
kable(go.test)

	set.size	n.both	n.up	n.down	p.value.both	p.value.up	p.value.down
GO:0016337	57	30	0	30	8.80e-22	1.00e+00	1.25e-28
GO:0098602	57	30	0	30	8.80e-22	1.00e+00	1.25e-28
GO:0009405	98	38	0	38	2.51e-21	1.00e+00	7.48e-30
GO:0007155	77	30	0	30	4.16e-17	1.00e+00	9.93e-24
GO:0020035	165	36	1	35	1.91e-11	9.87e-01	9.70e-18
GO:0044406	165	36	1	35	1.91e-11	9.87e-01	9.70e-18
GO:0022610	192	37	1	36	4.51e-10	9.94e-01	2.15e-16
GO:0051704	375	52	5	47	2.72e-08	9.68e-01	4.50e-14
GO:0020033	204	34	1	33	1.09e-07	9.95e-01	3.76e-13
GO:0051809	204	34	1	33	1.09e-07	9.95e-01	3.76e-13
GO:0043207	206	34	1	33	1.40e-07	9.96e-01	5.00e-13
GO:0051707	206	34	1	33	1.40e-07	9.96e-01	5.00e-13
GO:0051805	206	34	1	33	1.40e-07	9.96e-01	5.00e-13
GO:0051807	206	34	1	33	1.40e-07	9.96e-01	5.00e-13
GO:0051832	206	34	1	33	1.40e-07	9.96e-01	5.00e-13
GO:0051834	206	34	1	33	1.40e-07	9.96e-01	5.00e-13
GO:0052173	206	34	1	33	1.40e-07	9.96e-01	5.00e-13
GO:0052564	206	34	1	33	1.40e-07	9.96e-01	5.00e-13
GO:0009607	207	34	1	33	1.58e-07	9.96e-01	5.76e-13
GO:0020013	190	32	1	31	2.07e-07	9.93e-01	1.67e-12
GO:0022407	190	32	1	31	2.07e-07	9.93e-01	1.67e-12
GO:0030155	190	32	1	31	2.07e-07	9.93e-01	1.67e-12
GO:0034110	190	32	1	31	2.07e-07	9.93e-01	1.67e-12
GO:0034118	190	32	1	31	2.07e-07	9.93e-01	1.67e-12
GO:0044068	192	32	1	31	2.65e-07	9.94e-01	2.22e-12
GO:0044003	193	32	1	31	2.99e-07	9.94e-01	2.56e-12
GO:0051817	193	32	1	31	2.99e-07	9.94e-01	2.56e-12
GO:0035821	194	32	1	31	3.38e-07	9.94e-01	2.95e-12
GO:0009605	214	34	1	33	3.59e-07	9.96e-01	1.51e-12
GO:0065008	264	37	3	34	2.58e-06	9.68e-01	1.18e-10
GO:0044403	331	43	5	38	2.99e-06	9.32e-01	2.65e-10
GO:0044419	331	43	5	38	2.99e-06	9.32e-01	2.65e-10
GO:0051701	281	38	5	33	4.52e-06	8.52e-01	2.64e-09
GO:0050794	517	54	10	44	1.04e-04	8.62e-01	1.14e-07
GO:0050789	544	56	10	46	1.14e-04	9.00e-01	6.64e-08
GO:0050896	446	48	6	42	1.28e-04	9.76e-01	1.27e-08
GO:0065007	567	57	11	46	1.88e-04	8.70e-01	2.32e-07
GO:0044699	974	83	22	61	1.54e-03	7.71e-01	1.51e-05
GO:0032259	29	6	1	5	8.28e-03	5.28e-01	4.02e-03
GO:0008150	2653	189	56	133	9.98e-03	9.81e-01	1.86e-06
GO:0051336	22	5	3	2	1.04e-02	1.76e-02	1.99e-01
GO:0009894	23	5	3	2	1.27e-02	1.99e-02	2.13e-01
GO:0046578	18	4	2	2	2.35e-02	7.59e-02	1.45e-01
GO:0051056	18	4	2	2	2.35e-02	7.59e-02	1.45e-01
GO:1902531	18	4	2	2	2.35e-02	7.59e-02	1.45e-01
GO:0006289	11	3	2	1	2.80e-02	3.06e-02	3.43e-01
GO:0033124	19	4	3	1	2.83e-02	1.17e-02	5.17e-01
GO:0043087	19	4	3	1	2.83e-02	1.17e-02	5.17e-01
GO:0019220	28	5	3	2	2.86e-02	3.35e-02	2.83e-01
GO:0050790	28	5	3	2	2.86e-02	3.35e-02	2.83e-01
GO:0051174	28	5	3	2	2.86e-02	3.35e-02	2.83e-01
GO:0065009	28	5	3	2	2.86e-02	3.35e-02	2.83e-01
GO:0006140	20	4	3	1	3.36e-02	1.35e-02	5.35e-01
GO:0009118	20	4	3	1	3.36e-02	1.35e-02	5.35e-01
GO:0030811	20	4	3	1	3.36e-02	1.35e-02	5.35e-01
GO:0031329	20	4	3	1	3.36e-02	1.35e-02	5.35e-01
GO:0033121	20	4	3	1	3.36e-02	1.35e-02	5.35e-01
GO:1900542	20	4	3	1	3.36e-02	1.35e-02	5.35e-01
GO:0009396	5	2	0	2	3.49e-02	1.00e+00	1.30e-02
GO:0034968	5	2	0	2	3.49e-02	1.00e+00	1.30e-02
GO:0043414	21	4	1	3	3.96e-02	4.20e-01	4.20e-02
GO:0006396	223	21	8	13	4.07e-02	2.09e-01	7.48e-02
GO:0006414	22	4	1	3	4.60e-02	4.34e-01	4.74e-02
GO:0009966	22	4	2	2	4.60e-02	1.07e-01	1.99e-01
GO:0010646	22	4	2	2	4.60e-02	1.07e-01	1.99e-01
GO:0023051	22	4	2	2	4.60e-02	1.07e-01	1.99e-01
GO:0009132	6	2	2	0	5.02e-02	9.08e-03	1.00e+00
GO:0006760	6	2	0	2	5.02e-02	1.00e+00	1.90e-02
GO:0016571	6	2	0	2	5.02e-02	1.00e+00	1.90e-02
GO:0007018	23	4	1	3	5.31e-02	4.49e-01	5.30e-02
GO:0006457	81	9	1	8	6.72e-02	8.79e-01	1.05e-02
GO:0042559	7	2	0	2	6.74e-02	1.00e+00	2.60e-02
GO:0032318	16	3	2	1	7.54e-02	6.15e-02	4.58e-01
GO:0042558	8	2	0	2	8.62e-02	1.00e+00	3.38e-02
GO:0034660	137	13	5	8	8.97e-02	2.72e-01	1.42e-01
GO:0042254	86	9	3	6	9.05e-02	3.77e-01	1.03e-01
GO:0043248	9	2	1	1	1.06e-01	2.08e-01	2.91e-01
GO:0034470	92	9	4	5	1.24e-01	2.08e-01	2.62e-01
GO:0001510	10	2	1	1	1.28e-01	2.28e-01	3.18e-01
GO:0006479	10	2	0	2	1.28e-01	1.00e+00	5.17e-02
GO:0008213	10	2	0	2	1.28e-01	1.00e+00	5.17e-02
GO:0016568	20	3	0	3	1.28e-01	1.00e+00	3.70e-02
GO:0031323	161	14	6	8	1.36e-01	2.28e-01	2.57e-01
GO:0019222	175	15	6	9	1.38e-01	2.89e-01	2.10e-01
GO:0030260	56	6	4	2	1.39e-01	5.38e-02	6.27e-01
GO:0051806	56	6	4	2	1.39e-01	5.38e-02	6.27e-01
GO:0006928	44	5	2	3	1.41e-01	3.10e-01	2.27e-01
GO:0080090	163	14	6	8	1.46e-01	2.37e-01	2.67e-01
GO:0055114	109	10	5	5	1.48e-01	1.45e-01	3.89e-01
GO:0048583	33	4	2	2	1.51e-01	2.06e-01	3.53e-01
GO:0006397	97	9	3	6	1.56e-01	4.53e-01	1.56e-01
GO:0051246	34	4	0	4	1.63e-01	1.00e+00	3.70e-02
GO:0006399	85	8	3	5	1.65e-01	3.70e-01	2.13e-01
GO:0042398	12	2	0	2	1.72e-01	1.00e+00	7.21e-02
GO:0043648	12	2	0	2	1.72e-01	1.00e+00	7.21e-02
GO:0016569	12	2	0	2	1.72e-01	1.00e+00	7.21e-02
GO:0016570	12	2	0	2	1.72e-01	1.00e+00	7.21e-02
GO:0042176	3	1	0	1	1.77e-01	1.00e+00	1.08e-01
GO:0043086	3	1	0	1	1.77e-01	1.00e+00	1.08e-01
GO:0044092	3	1	0	1	1.77e-01	1.00e+00	1.08e-01
GO:0006848	3	1	0	1	1.77e-01	1.00e+00	1.08e-01
GO:0009438	3	1	1	0	1.77e-01	7.47e-02	1.00e+00
GO:0001817	3	1	0	1	1.77e-01	1.00e+00	1.08e-01
GO:0051239	3	1	0	1	1.77e-01	1.00e+00	1.08e-01
GO:0031167	3	1	0	1	1.77e-01	1.00e+00	1.08e-01
GO:0032312	3	1	1	0	1.77e-01	7.47e-02	1.00e+00
GO:0042026	3	1	0	1	1.77e-01	1.00e+00	1.08e-01
GO:0008154	3	1	0	1	1.77e-01	1.00e+00	1.08e-01
GO:0006213	3	1	1	0	1.77e-01	7.47e-02	1.00e+00
GO:0009218	3	1	1	0	1.77e-01	7.47e-02	1.00e+00
GO:0009220	3	1	1	0	1.77e-01	7.47e-02	1.00e+00
GO:0046131	3	1	1	0	1.77e-01	7.47e-02	1.00e+00
GO:0046132	3	1	1	0	1.77e-01	7.47e-02	1.00e+00
GO:0046134	3	1	1	0	1.77e-01	7.47e-02	1.00e+00
GO:0006165	3	1	1	0	1.77e-01	7.47e-02	1.00e+00
GO:0009148	3	1	1	0	1.77e-01	7.47e-02	1.00e+00
GO:0046939	3	1	1	0	1.77e-01	7.47e-02	1.00e+00
GO:1901070	3	1	1	0	1.77e-01	7.47e-02	1.00e+00
GO:0007006	3	1	0	1	1.77e-01	1.00e+00	1.08e-01
GO:0007007	3	1	0	1	1.77e-01	1.00e+00	1.08e-01
GO:0045039	3	1	0	1	1.77e-01	1.00e+00	1.08e-01
GO:0090151	3	1	0	1	1.77e-01	1.00e+00	1.08e-01
GO:0006275	3	1	1	0	1.77e-01	7.47e-02	1.00e+00
GO:0006520	87	8	1	7	1.81e-01	8.96e-01	4.39e-02
GO:0045454	36	4	1	3	1.89e-01	6.07e-01	1.51e-01
GO:0006417	24	3	0	3	1.90e-01	1.00e+00	5.90e-02
GO:0016070	404	30	12	18	1.94e-01	3.35e-01	2.55e-01
GO:0019725	49	5	2	3	1.94e-01	3.57e-01	2.78e-01
GO:0044409	62	6	4	2	1.94e-01	7.29e-02	6.82e-01
GO:0051828	62	6	4	2	1.94e-01	7.29e-02	6.82e-01
GO:0032313	13	2	1	1	1.96e-01	2.86e-01	3.92e-01
GO:0032483	13	2	1	1	1.96e-01	2.86e-01	3.92e-01
GO:0016579	13	2	1	1	1.96e-01	2.86e-01	3.92e-01
GO:0070646	13	2	1	1	1.96e-01	2.86e-01	3.92e-01
GO:0016071	104	9	3	6	2.08e-01	4.99e-01	1.95e-01
GO:0022613	105	9	3	6	2.15e-01	5.05e-01	2.00e-01
GO:0006511	78	7	2	5	2.19e-01	5.97e-01	1.68e-01
GO:1901607	14	2	0	2	2.19e-01	1.00e+00	9.48e-02
GO:0006575	14	2	0	2	2.19e-01	1.00e+00	9.48e-02
GO:0015914	4	1	0	1	2.29e-01	1.00e+00	1.42e-01
GO:0031365	4	1	0	1	2.29e-01	1.00e+00	1.42e-01
GO:0090501	4	1	0	1	2.29e-01	1.00e+00	1.42e-01
GO:0006338	4	1	0	1	2.29e-01	1.00e+00	1.42e-01
GO:0006904	4	1	1	0	2.29e-01	9.83e-02	1.00e+00
GO:0022406	4	1	1	0	2.29e-01	9.83e-02	1.00e+00
GO:0048278	4	1	1	0	2.29e-01	9.83e-02	1.00e+00
GO:0051052	4	1	1	0	2.29e-01	9.83e-02	1.00e+00
GO:0032012	4	1	1	0	2.29e-01	9.83e-02	1.00e+00
GO:0009147	4	1	1	0	2.29e-01	9.83e-02	1.00e+00
GO:0002097	4	1	1	0	2.29e-01	9.83e-02	1.00e+00
GO:0002098	4	1	1	0	2.29e-01	9.83e-02	1.00e+00
GO:0043650	4	1	0	1	2.29e-01	1.00e+00	1.42e-01
GO:0006875	4	1	1	0	2.29e-01	9.83e-02	1.00e+00
GO:0055065	4	1	1	0	2.29e-01	9.83e-02	1.00e+00
GO:0008616	4	1	0	1	2.29e-01	1.00e+00	1.42e-01
GO:0046116	4	1	0	1	2.29e-01	1.00e+00	1.42e-01
GO:0051028	4	1	0	1	2.29e-01	1.00e+00	1.42e-01
GO:0016925	4	1	0	1	2.29e-01	1.00e+00	1.42e-01
GO:0009186	4	1	1	0	2.29e-01	9.83e-02	1.00e+00
GO:0006656	4	1	0	1	2.29e-01	1.00e+00	1.42e-01
GO:0046470	4	1	0	1	2.29e-01	1.00e+00	1.42e-01
GO:0030163	93	8	3	5	2.31e-01	4.26e-01	2.69e-01
GO:0019941	80	7	2	5	2.38e-01	6.11e-01	1.80e-01
GO:0043632	80	7	2	5	2.38e-01	6.11e-01	1.80e-01
GO:0006364	53	5	2	3	2.40e-01	3.94e-01	3.20e-01
GO:0016072	53	5	2	3	2.40e-01	3.94e-01	3.20e-01
GO:0010608	27	3	0	3	2.40e-01	1.00e+00	7.86e-02
GO:0007017	40	4	1	3	2.43e-01	6.46e-01	1.88e-01
GO:0008033	40	4	2	2	2.43e-01	2.72e-01	4.46e-01
GO:0042592	54	5	2	3	2.52e-01	4.03e-01	3.30e-01
GO:0071705	16	2	0	2	2.67e-01	1.00e+00	1.19e-01
GO:0044257	83	7	2	5	2.67e-01	6.31e-01	2.00e-01
GO:0051603	83	7	2	5	2.67e-01	6.31e-01	2.00e-01
GO:0006378	5	1	1	0	2.78e-01	1.21e-01	1.00e+00
GO:0031124	5	1	1	0	2.78e-01	1.21e-01	1.00e+00
GO:0006887	5	1	1	0	2.78e-01	1.21e-01	1.00e+00
GO:0032940	5	1	1	0	2.78e-01	1.21e-01	1.00e+00
GO:0046903	5	1	1	0	2.78e-01	1.21e-01	1.00e+00
GO:0009263	5	1	1	0	2.78e-01	1.21e-01	1.00e+00
GO:0006207	5	1	0	1	2.78e-01	1.00e+00	1.74e-01
GO:0019856	5	1	0	1	2.78e-01	1.00e+00	1.74e-01
GO:0046112	5	1	0	1	2.78e-01	1.00e+00	1.74e-01
GO:0006094	5	1	0	1	2.78e-01	1.00e+00	1.74e-01
GO:0042439	5	1	0	1	2.78e-01	1.00e+00	1.74e-01
GO:0006813	5	1	1	0	2.78e-01	1.21e-01	1.00e+00
GO:0008380	85	7	1	6	2.88e-01	8.91e-01	9.85e-02
GO:0072528	17	2	1	1	2.91e-01	3.56e-01	4.78e-01
GO:0032268	30	3	0	3	2.93e-01	1.00e+00	1.01e-01
GO:1901605	30	3	0	3	2.93e-01	1.00e+00	1.01e-01
GO:0019219	129	10	6	4	2.95e-01	1.11e-01	7.20e-01
GO:0051171	129	10	6	4	2.95e-01	1.11e-01	7.20e-01
GO:0006325	31	3	0	3	3.10e-01	1.00e+00	1.09e-01
GO:0070647	31	3	1	2	3.10e-01	5.52e-01	3.25e-01
GO:0052126	73	6	4	2	3.12e-01	1.15e-01	7.66e-01
GO:0052192	73	6	4	2	3.12e-01	1.15e-01	7.66e-01
GO:0042493	59	5	0	5	3.14e-01	1.00e+00	6.91e-02
GO:0043038	45	4	1	3	3.15e-01	6.89e-01	2.37e-01
GO:0043039	45	4	1	3	3.15e-01	6.89e-01	2.37e-01
GO:0009451	45	4	2	2	3.15e-01	3.20e-01	5.08e-01
GO:0072527	18	2	1	1	3.15e-01	3.73e-01	4.98e-01
GO:0006096	18	2	0	2	3.15e-01	1.00e+00	1.45e-01
GO:0044085	176	13	6	7	3.16e-01	2.93e-01	4.92e-01
GO:0015748	6	1	0	1	3.23e-01	1.00e+00	2.05e-01
GO:0043631	6	1	1	0	3.23e-01	1.44e-01	1.00e+00
GO:0071976	6	1	1	0	3.23e-01	1.44e-01	1.00e+00
GO:0007275	6	1	1	0	3.23e-01	1.44e-01	1.00e+00
GO:0000154	6	1	0	1	3.23e-01	1.00e+00	2.05e-01
GO:0070682	6	1	0	1	3.23e-01	1.00e+00	2.05e-01
GO:0045892	6	1	0	1	3.23e-01	1.00e+00	2.05e-01
GO:0045934	6	1	0	1	3.23e-01	1.00e+00	2.05e-01
GO:0051172	6	1	0	1	3.23e-01	1.00e+00	2.05e-01
GO:0051253	6	1	0	1	3.23e-01	1.00e+00	2.05e-01
GO:1902679	6	1	0	1	3.23e-01	1.00e+00	2.05e-01
GO:0006730	6	1	0	1	3.23e-01	1.00e+00	2.05e-01
GO:0009452	6	1	0	1	3.23e-01	1.00e+00	2.05e-01
GO:0036260	6	1	0	1	3.23e-01	1.00e+00	2.05e-01
GO:0007015	6	1	0	1	3.23e-01	1.00e+00	2.05e-01
GO:0006206	6	1	0	1	3.23e-01	1.00e+00	2.05e-01
GO:0044743	6	1	0	1	3.23e-01	1.00e+00	2.05e-01
GO:0006536	6	1	0	1	3.23e-01	1.00e+00	2.05e-01
GO:0019319	6	1	0	1	3.23e-01	1.00e+00	2.05e-01
GO:0046364	6	1	0	1	3.23e-01	1.00e+00	2.05e-01
GO:0010467	619	42	18	24	3.26e-01	3.14e-01	4.64e-01
GO:0006281	60	5	3	2	3.27e-01	1.97e-01	6.65e-01
GO:0051276	46	4	0	4	3.29e-01	1.00e+00	9.24e-02
GO:0015711	19	2	0	2	3.39e-01	1.00e+00	1.58e-01
GO:0006099	19	2	2	0	3.39e-01	8.34e-02	1.00e+00
GO:0006974	61	5	3	2	3.40e-01	2.04e-01	6.74e-01
GO:0044265	105	8	3	5	3.42e-01	5.05e-01	3.59e-01
GO:0006950	107	8	4	4	3.61e-01	2.91e-01	5.75e-01
GO:0006400	20	2	1	1	3.62e-01	4.04e-01	5.35e-01
GO:0009060	20	2	2	0	3.62e-01	9.12e-02	1.00e+00
GO:0044707	7	1	1	0	3.66e-01	1.66e-01	1.00e+00
GO:0016042	7	1	1	0	3.66e-01	1.66e-01	1.00e+00
GO:0010558	7	1	0	1	3.66e-01	1.00e+00	2.35e-01
GO:2000113	7	1	0	1	3.66e-01	1.00e+00	2.35e-01
GO:0006403	7	1	0	1	3.66e-01	1.00e+00	2.35e-01
GO:0050657	7	1	0	1	3.66e-01	1.00e+00	2.35e-01
GO:0050658	7	1	0	1	3.66e-01	1.00e+00	2.35e-01
GO:0051236	7	1	0	1	3.66e-01	1.00e+00	2.35e-01
GO:0046165	7	1	0	1	3.66e-01	1.00e+00	2.35e-01
GO:0009112	7	1	0	1	3.66e-01	1.00e+00	2.35e-01
GO:0051259	7	1	1	0	3.66e-01	1.66e-01	1.00e+00
GO:0006637	7	1	1	0	3.66e-01	1.66e-01	1.00e+00
GO:0035383	7	1	1	0	3.66e-01	1.66e-01	1.00e+00
GO:0020027	7	1	1	0	3.66e-01	1.66e-01	1.00e+00
GO:0042540	7	1	1	0	3.66e-01	1.66e-01	1.00e+00
GO:0006091	49	4	2	2	3.73e-01	3.57e-01	5.54e-01
GO:0009057	109	8	3	5	3.81e-01	5.31e-01	3.89e-01
GO:0048519	21	2	0	2	3.85e-01	1.00e+00	1.85e-01
GO:0033554	65	5	3	2	3.91e-01	2.30e-01	7.07e-01
GO:0040011	81	6	4	2	4.03e-01	1.52e-01	8.14e-01
GO:0042221	81	6	0	6	4.03e-01	1.00e+00	8.24e-02
GO:0090304	529	35	14	21	4.06e-01	4.86e-01	4.25e-01
GO:0006081	8	1	1	0	4.06e-01	1.87e-01	1.00e+00
GO:0032501	8	1	1	0	4.06e-01	1.87e-01	1.00e+00
GO:0015718	8	1	0	1	4.06e-01	1.00e+00	2.64e-01
GO:0009890	8	1	0	1	4.06e-01	1.00e+00	2.64e-01
GO:0031327	8	1	0	1	4.06e-01	1.00e+00	2.64e-01
GO:0009262	8	1	1	0	4.06e-01	1.87e-01	1.00e+00
GO:0009408	22	2	1	1	4.08e-01	4.34e-01	5.69e-01
GO:0044260	1161	75	28	47	4.24e-01	6.66e-01	3.00e-01
GO:0009266	23	2	1	1	4.30e-01	4.49e-01	5.86e-01
GO:1902589	53	4	0	4	4.31e-01	1.00e+00	1.36e-01
GO:0010556	130	9	3	6	4.36e-01	6.51e-01	3.61e-01
GO:2000112	130	9	3	6	4.36e-01	6.51e-01	3.61e-01
GO:0031123	9	1	1	0	4.44e-01	2.08e-01	1.00e+00
GO:0006221	9	1	1	0	4.44e-01	2.08e-01	1.00e+00
GO:0006897	9	1	0	1	4.44e-01	1.00e+00	2.91e-01
GO:0010629	9	1	0	1	4.44e-01	1.00e+00	2.91e-01
GO:0006066	9	1	0	1	4.44e-01	1.00e+00	2.91e-01
GO:0009889	131	9	3	6	4.45e-01	6.56e-01	3.68e-01
GO:0031326	131	9	3	6	4.45e-01	6.56e-01	3.68e-01
GO:0071840	287	19	6	13	4.46e-01	7.49e-01	2.79e-01
GO:0009628	24	2	1	1	4.52e-01	4.63e-01	6.01e-01
GO:0008652	24	2	0	2	4.52e-01	1.00e+00	2.27e-01
GO:0018130	195	13	6	7	4.59e-01	3.80e-01	6.03e-01
GO:0006090	25	2	0	2	4.74e-01	1.00e+00	2.41e-01
GO:0016052	25	2	0	2	4.74e-01	1.00e+00	2.41e-01
GO:0044724	25	2	0	2	4.74e-01	1.00e+00	2.41e-01
GO:0060255	150	10	3	7	4.75e-01	7.43e-01	3.32e-01
GO:1901566	103	7	2	5	4.75e-01	7.45e-01	3.43e-01
GO:0006220	10	1	1	0	4.79e-01	2.28e-01	1.00e+00
GO:0006465	10	1	0	1	4.79e-01	1.00e+00	3.18e-01
GO:0031324	10	1	0	1	4.79e-01	1.00e+00	3.18e-01
GO:0006576	10	1	0	1	4.79e-01	1.00e+00	3.18e-01
GO:0009308	10	1	0	1	4.79e-01	1.00e+00	3.18e-01
GO:0044106	10	1	0	1	4.79e-01	1.00e+00	3.18e-01
GO:0007166	10	1	0	1	4.79e-01	1.00e+00	3.18e-01
GO:0030036	10	1	0	1	4.79e-01	1.00e+00	3.18e-01
GO:0006779	10	1	1	0	4.79e-01	2.28e-01	1.00e+00
GO:0006783	10	1	1	0	4.79e-01	2.28e-01	1.00e+00
GO:1901362	199	13	6	7	4.89e-01	3.98e-01	6.24e-01
GO:0019752	152	10	1	9	4.92e-01	9.81e-01	1.16e-01
GO:0044271	200	13	6	7	4.96e-01	4.03e-01	6.29e-01
GO:0051188	42	3	1	2	4.99e-01	6.64e-01	4.71e-01
GO:0006082	154	10	1	9	5.09e-01	9.82e-01	1.23e-01
GO:0043436	154	10	1	9	5.09e-01	9.82e-01	1.23e-01
GO:0015931	11	1	0	1	5.12e-01	1.00e+00	3.43e-01
GO:0006869	11	1	0	1	5.12e-01	1.00e+00	3.43e-01
GO:0006720	11	1	0	1	5.12e-01	1.00e+00	3.43e-01
GO:0008299	11	1	0	1	5.12e-01	1.00e+00	3.43e-01
GO:0090305	11	1	0	1	5.12e-01	1.00e+00	3.43e-01
GO:0046148	11	1	1	0	5.12e-01	2.48e-01	1.00e+00
GO:0072657	11	1	0	1	5.12e-01	1.00e+00	3.43e-01
GO:0090150	11	1	0	1	5.12e-01	1.00e+00	3.43e-01
GO:0044767	11	1	1	0	5.12e-01	2.48e-01	1.00e+00
GO:0007059	11	1	1	0	5.12e-01	2.48e-01	1.00e+00
GO:0000413	11	1	0	1	5.12e-01	1.00e+00	3.43e-01
GO:0018208	11	1	0	1	5.12e-01	1.00e+00	3.43e-01
GO:0006873	11	1	1	0	5.12e-01	2.48e-01	1.00e+00
GO:0030003	11	1	1	0	5.12e-01	2.48e-01	1.00e+00
GO:1901617	11	1	0	1	5.12e-01	1.00e+00	3.43e-01
GO:0033014	11	1	1	0	5.12e-01	2.48e-01	1.00e+00
GO:0009064	11	1	0	1	5.12e-01	1.00e+00	3.43e-01
GO:0006418	43	3	1	2	5.15e-01	6.72e-01	4.84e-01
GO:0051186	59	4	2	2	5.15e-01	4.47e-01	6.56e-01
GO:0018193	28	2	1	1	5.35e-01	5.16e-01	6.58e-01
GO:0019438	190	12	6	6	5.41e-01	3.57e-01	7.24e-01
GO:0010876	12	1	0	1	5.43e-01	1.00e+00	3.68e-01
GO:0018345	12	1	1	0	5.43e-01	2.67e-01	1.00e+00
GO:0016226	12	1	1	0	5.43e-01	2.67e-01	1.00e+00
GO:0031163	12	1	1	0	5.43e-01	2.67e-01	1.00e+00
GO:0032502	12	1	1	0	5.43e-01	2.67e-01	1.00e+00
GO:0050801	12	1	1	0	5.43e-01	2.67e-01	1.00e+00
GO:0055080	12	1	1	0	5.43e-01	2.67e-01	1.00e+00
GO:0055082	12	1	1	0	5.43e-01	2.67e-01	1.00e+00
GO:0010605	12	1	0	1	5.43e-01	1.00e+00	3.68e-01
GO:0030029	12	1	0	1	5.43e-01	1.00e+00	3.68e-01
GO:0016051	12	1	0	1	5.43e-01	1.00e+00	3.68e-01
GO:0006006	12	1	0	1	5.43e-01	1.00e+00	3.68e-01
GO:0006732	45	3	1	2	5.46e-01	6.89e-01	5.08e-01
GO:0044710	512	32	12	20	5.49e-01	6.67e-01	4.59e-01
GO:0045333	29	2	2	0	5.54e-01	1.68e-01	1.00e+00
GO:0006820	46	3	0	3	5.61e-01	1.00e+00	2.48e-01
GO:0006508	161	10	3	7	5.67e-01	7.86e-01	4.00e-01
GO:0071822	63	4	2	2	5.68e-01	4.81e-01	6.91e-01
GO:0065002	13	1	0	1	5.71e-01	1.00e+00	3.92e-01
GO:0006986	13	1	0	1	5.71e-01	1.00e+00	3.92e-01
GO:0035966	13	1	0	1	5.71e-01	1.00e+00	3.92e-01
GO:0009892	13	1	0	1	5.71e-01	1.00e+00	3.92e-01
GO:0006778	13	1	1	0	5.71e-01	2.86e-01	1.00e+00
GO:0042168	13	1	1	0	5.71e-01	2.86e-01	1.00e+00
GO:0015980	30	2	2	0	5.73e-01	1.78e-01	1.00e+00
GO:0043170	1238	77	28	49	5.76e-01	7.97e-01	3.58e-01
GO:0009165	47	3	2	1	5.76e-01	3.38e-01	8.35e-01
GO:0006650	31	2	0	2	5.91e-01	1.00e+00	3.25e-01
GO:1901293	48	3	2	1	5.91e-01	3.48e-01	8.42e-01
GO:0015849	14	1	0	1	5.98e-01	1.00e+00	4.15e-01
GO:0046942	14	1	0	1	5.98e-01	1.00e+00	4.15e-01
GO:0042440	14	1	1	0	5.98e-01	3.04e-01	1.00e+00
GO:0044802	14	1	0	1	5.98e-01	1.00e+00	4.15e-01
GO:0006518	14	1	0	1	5.98e-01	1.00e+00	4.15e-01
GO:0016485	14	1	0	1	5.98e-01	1.00e+00	4.15e-01
GO:0048878	14	1	1	0	5.98e-01	3.04e-01	1.00e+00
GO:0048523	14	1	0	1	5.98e-01	1.00e+00	4.15e-01
GO:0005996	14	1	0	1	5.98e-01	1.00e+00	4.15e-01
GO:0019318	14	1	0	1	5.98e-01	1.00e+00	4.15e-01
GO:0033013	14	1	1	0	5.98e-01	3.04e-01	1.00e+00
GO:0006626	14	1	0	1	5.98e-01	1.00e+00	4.15e-01
GO:0070585	14	1	0	1	5.98e-01	1.00e+00	4.15e-01
GO:0072655	14	1	0	1	5.98e-01	1.00e+00	4.15e-01
GO:1901575	182	11	4	7	6.03e-01	6.89e-01	5.28e-01
GO:0000375	66	4	0	4	6.05e-01	1.00e+00	2.34e-01
GO:0044267	686	42	14	28	6.08e-01	8.51e-01	3.44e-01
GO:0009163	32	2	1	1	6.08e-01	5.64e-01	7.07e-01
GO:0042455	32	2	1	1	6.08e-01	5.64e-01	7.07e-01
GO:0046486	32	2	0	2	6.08e-01	1.00e+00	3.39e-01
GO:0009108	32	2	0	2	6.08e-01	1.00e+00	3.39e-01
GO:0044711	184	11	3	8	6.18e-01	8.55e-01	3.86e-01
GO:0006461	50	3	2	1	6.19e-01	3.66e-01	8.53e-01
GO:0070271	50	3	2	1	6.19e-01	3.66e-01	8.53e-01
GO:1901659	33	2	1	1	6.25e-01	5.75e-01	7.18e-01
GO:0043623	33	2	1	1	6.25e-01	5.75e-01	7.18e-01
GO:0044763	725	44	17	27	6.34e-01	6.86e-01	5.48e-01
GO:1901564	220	13	3	10	6.38e-01	9.25e-01	3.11e-01
GO:0010468	137	8	2	6	6.41e-01	8.70e-01	4.09e-01
GO:0009056	188	11	4	7	6.47e-01	7.14e-01	5.63e-01
GO:0034641	696	42	16	26	6.47e-01	7.13e-01	5.41e-01
GO:0009201	16	1	1	0	6.48e-01	3.39e-01	1.00e+00
GO:0009206	16	1	1	0	6.48e-01	3.39e-01	1.00e+00
GO:0010033	16	1	0	1	6.48e-01	1.00e+00	4.58e-01
GO:1901615	16	1	0	1	6.48e-01	1.00e+00	4.58e-01
GO:0043933	122	7	2	5	6.57e-01	8.24e-01	4.85e-01
GO:0006259	140	8	5	3	6.65e-01	2.86e-01	9.02e-01
GO:0009145	17	1	1	0	6.70e-01	3.56e-01	1.00e+00
GO:0061024	17	1	0	1	6.70e-01	1.00e+00	4.78e-01
GO:0048870	17	1	1	0	6.70e-01	3.56e-01	1.00e+00
GO:0051674	17	1	1	0	6.70e-01	3.56e-01	1.00e+00
GO:0031338	17	1	1	0	6.70e-01	3.56e-01	1.00e+00
GO:0007005	17	1	0	1	6.70e-01	1.00e+00	4.78e-01
GO:0006725	672	40	16	24	6.80e-01	6.57e-01	6.35e-01
GO:0008152	1658	101	38	63	6.83e-01	8.13e-01	4.76e-01
GO:0046483	674	40	16	24	6.88e-01	6.62e-01	6.41e-01
GO:0016192	91	5	3	2	6.88e-01	4.12e-01	8.62e-01
GO:0009142	18	1	1	0	6.91e-01	3.73e-01	1.00e+00
GO:0071806	18	1	0	1	6.91e-01	1.00e+00	4.98e-01
GO:0032446	18	1	0	1	6.91e-01	1.00e+00	4.98e-01
GO:0034654	161	9	5	4	6.95e-01	3.93e-01	8.61e-01
GO:0006807	725	43	16	27	6.95e-01	7.72e-01	5.48e-01
GO:1901360	678	40	16	24	7.02e-01	6.72e-01	6.53e-01
GO:0006886	111	6	2	4	7.10e-01	7.82e-01	6.04e-01
GO:0051604	19	1	0	1	7.10e-01	1.00e+00	5.17e-01
GO:0006839	19	1	0	1	7.10e-01	1.00e+00	5.17e-01
GO:0046907	146	8	3	5	7.10e-01	7.27e-01	6.46e-01
GO:0044237	1477	89	33	56	7.14e-01	8.41e-01	4.88e-01
GO:0043543	20	1	1	0	7.29e-01	4.04e-01	1.00e+00
GO:0017038	20	1	0	1	7.29e-01	1.00e+00	5.35e-01
GO:0043603	20	1	0	1	7.29e-01	1.00e+00	5.35e-01
GO:0051649	150	8	3	5	7.38e-01	7.43e-01	6.70e-01
GO:0006139	639	37	15	22	7.39e-01	6.76e-01	7.00e-01
GO:0019538	771	45	15	30	7.40e-01	9.02e-01	4.43e-01
GO:0034613	115	6	2	4	7.41e-01	7.98e-01	6.32e-01
GO:0070727	115	6	2	4	7.41e-01	7.98e-01	6.32e-01
GO:0044248	151	8	3	5	7.45e-01	7.48e-01	6.75e-01
GO:0046039	21	1	1	0	7.46e-01	4.20e-01	1.00e+00
GO:0046474	21	1	0	1	7.46e-01	1.00e+00	5.53e-01
GO:0000377	61	3	0	3	7.49e-01	1.00e+00	4.02e-01
GO:0000398	61	3	0	3	7.49e-01	1.00e+00	4.02e-01
GO:0009987	1767	106	39	67	7.55e-01	8.86e-01	4.82e-01
GO:0044238	1510	90	32	58	7.57e-01	9.12e-01	4.41e-01
GO:0006351	99	5	3	2	7.57e-01	4.66e-01	8.92e-01
GO:1901068	22	1	1	0	7.62e-01	4.34e-01	1.00e+00
GO:0006366	22	1	1	0	7.62e-01	4.34e-01	1.00e+00
GO:0045017	22	1	0	1	7.62e-01	1.00e+00	5.69e-01
GO:0006310	22	1	1	0	7.62e-01	4.34e-01	1.00e+00
GO:0051716	136	7	4	3	7.63e-01	4.60e-01	8.91e-01
GO:0006644	43	2	0	2	7.64e-01	1.00e+00	4.84e-01
GO:0051641	154	8	3	5	7.64e-01	7.59e-01	6.92e-01
GO:0090407	82	4	2	2	7.69e-01	6.24e-01	8.19e-01
GO:0030001	23	1	1	0	7.77e-01	4.49e-01	1.00e+00
GO:0006790	23	1	1	0	7.77e-01	4.49e-01	1.00e+00
GO:0006355	102	5	2	3	7.80e-01	7.40e-01	7.43e-01
GO:2001141	102	5	2	3	7.80e-01	7.40e-01	7.43e-01
GO:0055086	103	5	2	3	7.87e-01	7.45e-01	7.49e-01
GO:0032774	103	5	3	2	7.87e-01	4.92e-01	9.04e-01
GO:0046488	24	1	0	1	7.91e-01	1.00e+00	6.01e-01
GO:0051252	105	5	2	3	8.01e-01	7.55e-01	7.61e-01
GO:0043412	303	16	6	10	8.07e-01	7.94e-01	7.09e-01
GO:0006412	286	15	7	8	8.09e-01	6.01e-01	8.50e-01
GO:0006996	125	6	0	6	8.09e-01	1.00e+00	3.28e-01
GO:0044712	68	3	1	2	8.12e-01	8.30e-01	7.31e-01
GO:0016053	48	2	0	2	8.15e-01	1.00e+00	5.43e-01
GO:0046394	48	2	0	2	8.15e-01	1.00e+00	5.43e-01
GO:0006817	26	1	0	1	8.17e-01	1.00e+00	6.31e-01
GO:0033043	26	1	1	0	8.17e-01	4.90e-01	1.00e+00
GO:0071704	1555	91	33	58	8.21e-01	9.15e-01	5.46e-01
GO:0071702	201	10	2	8	8.25e-01	9.68e-01	4.84e-01
GO:0015698	27	1	0	1	8.28e-01	1.00e+00	6.45e-01
GO:0007010	27	1	0	1	8.28e-01	1.00e+00	6.45e-01
GO:0009152	27	1	1	0	8.28e-01	5.03e-01	1.00e+00
GO:0034220	27	1	0	1	8.28e-01	1.00e+00	6.45e-01
GO:0042451	27	1	1	0	8.28e-01	5.03e-01	1.00e+00
GO:0046129	27	1	1	0	8.28e-01	5.03e-01	1.00e+00
GO:0060627	27	1	1	0	8.28e-01	5.03e-01	1.00e+00
GO:0006497	27	1	1	0	8.28e-01	5.03e-01	1.00e+00
GO:0042157	27	1	1	0	8.28e-01	5.03e-01	1.00e+00
GO:0042158	27	1	1	0	8.28e-01	5.03e-01	1.00e+00
GO:0048193	27	1	1	0	8.28e-01	5.03e-01	1.00e+00
GO:0044723	50	2	0	2	8.33e-01	1.00e+00	5.65e-01
GO:0033036	186	9	2	7	8.39e-01	9.55e-01	5.52e-01
GO:0009260	28	1	1	0	8.39e-01	5.16e-01	1.00e+00
GO:0044283	73	3	0	3	8.48e-01	1.00e+00	5.20e-01
GO:0006164	29	1	1	0	8.49e-01	5.28e-01	1.00e+00
GO:0046390	29	1	1	0	8.49e-01	5.28e-01	1.00e+00
GO:0051128	29	1	1	0	8.49e-01	5.28e-01	1.00e+00
GO:0044281	279	14	3	11	8.50e-01	9.77e-01	4.77e-01
GO:0008654	30	1	0	1	8.59e-01	1.00e+00	6.83e-01
GO:0051301	30	1	1	0	8.59e-01	5.41e-01	1.00e+00
GO:0032879	31	1	1	0	8.68e-01	5.52e-01	1.00e+00
GO:0051049	31	1	1	0	8.68e-01	5.52e-01	1.00e+00
GO:0051726	31	1	0	1	8.68e-01	1.00e+00	6.95e-01
GO:0016043	213	10	3	7	8.73e-01	9.15e-01	6.94e-01
GO:0015672	32	1	1	0	8.76e-01	5.64e-01	1.00e+00
GO:0006413	56	2	1	1	8.77e-01	7.67e-01	8.84e-01
GO:1901137	78	3	2	1	8.78e-01	5.97e-01	9.50e-01
GO:0006812	57	2	1	1	8.83e-01	7.73e-01	8.88e-01
GO:0006260	57	2	1	1	8.83e-01	7.73e-01	8.88e-01
GO:0072522	33	1	1	0	8.84e-01	5.75e-01	1.00e+00
GO:0072594	33	1	0	1	8.84e-01	1.00e+00	7.18e-01
GO:0022607	100	4	3	1	8.84e-01	4.73e-01	9.79e-01
GO:0006811	101	4	1	3	8.89e-01	9.28e-01	7.37e-01
GO:1902580	34	1	0	1	8.91e-01	1.00e+00	7.28e-01
GO:0033365	35	1	0	1	8.98e-01	1.00e+00	7.39e-01
GO:0006464	258	12	4	8	8.99e-01	9.02e-01	7.60e-01
GO:0036211	258	12	4	8	8.99e-01	9.02e-01	7.60e-01
GO:0009119	60	2	1	1	9.00e-01	7.90e-01	9.00e-01
GO:0015031	164	7	2	5	9.01e-01	9.27e-01	7.44e-01
GO:0065003	83	3	2	1	9.03e-01	6.31e-01	9.59e-01
GO:0045184	165	7	2	5	9.04e-01	9.28e-01	7.49e-01
GO:0006605	36	1	0	1	9.05e-01	1.00e+00	7.48e-01
GO:0009116	61	2	1	1	9.05e-01	7.95e-01	9.04e-01
GO:0005975	61	2	0	2	9.05e-01	1.00e+00	6.74e-01
GO:0055085	84	3	1	2	9.07e-01	8.88e-01	8.30e-01
GO:1901657	62	2	1	1	9.10e-01	8.01e-01	9.08e-01
GO:0032787	63	2	0	2	9.15e-01	1.00e+00	6.91e-01
GO:0008104	170	7	2	5	9.19e-01	9.36e-01	7.72e-01
GO:0006629	110	4	1	3	9.23e-01	9.43e-01	7.88e-01
GO:0009117	89	3	2	1	9.26e-01	6.69e-01	9.68e-01
GO:0008610	66	2	0	2	9.27e-01	1.00e+00	7.15e-01
GO:0006753	91	3	2	1	9.33e-01	6.81e-01	9.70e-01
GO:0009199	42	1	1	0	9.36e-01	6.64e-01	1.00e+00
GO:0009205	42	1	1	0	9.36e-01	6.64e-01	1.00e+00
GO:0009144	43	1	1	0	9.40e-01	6.72e-01	1.00e+00
GO:0034645	480	23	12	11	9.40e-01	5.75e-01	9.77e-01
GO:0044255	94	3	0	3	9.42e-01	1.00e+00	6.91e-01
GO:0009059	482	23	12	11	9.43e-01	5.81e-01	9.78e-01
GO:0007165	71	2	1	1	9.44e-01	8.42e-01	9.35e-01
GO:0023052	71	2	1	1	9.44e-01	8.42e-01	9.35e-01
GO:0044700	71	2	1	1	9.44e-01	8.42e-01	9.35e-01
GO:0007049	45	1	1	0	9.47e-01	6.89e-01	1.00e+00
GO:0034622	72	2	1	1	9.47e-01	8.46e-01	9.37e-01
GO:0009141	46	1	1	0	9.51e-01	6.97e-01	1.00e+00
GO:1901576	650	32	14	18	9.52e-01	7.90e-01	9.39e-01
GO:0019637	143	5	2	3	9.53e-01	8.86e-01	9.10e-01
GO:0009058	669	33	15	18	9.53e-01	7.44e-01	9.55e-01
GO:0016310	122	4	2	2	9.55e-01	8.24e-01	9.47e-01
GO:0007154	77	2	1	1	9.60e-01	8.65e-01	9.48e-01
GO:0044249	647	31	14	17	9.65e-01	7.84e-01	9.61e-01
GO:0009150	55	1	1	0	9.73e-01	7.60e-01	1.00e+00
GO:0042278	55	1	1	0	9.73e-01	7.60e-01	1.00e+00
GO:0046128	55	1	1	0	9.73e-01	7.60e-01	1.00e+00
GO:1902582	84	2	1	1	9.73e-01	8.88e-01	9.61e-01
GO:0006468	110	3	1	2	9.73e-01	9.43e-01	9.23e-01
GO:0009259	56	1	1	0	9.74e-01	7.67e-01	1.00e+00
GO:0019693	57	1	1	0	9.76e-01	7.73e-01	1.00e+00
GO:0006810	404	17	6	11	9.77e-01	9.52e-01	9.02e-01
GO:0051234	405	17	6	11	9.77e-01	9.53e-01	9.03e-01
GO:0006163	58	1	1	0	9.78e-01	7.79e-01	1.00e+00
GO:0051179	426	18	7	11	9.79e-01	9.27e-01	9.33e-01
GO:0044765	233	8	4	4	9.83e-01	8.53e-01	9.78e-01
GO:0072521	64	1	1	0	9.85e-01	8.11e-01	1.00e+00
GO:1902578	238	8	4	4	9.86e-01	8.64e-01	9.81e-01
GO:1901135	125	3	2	1	9.88e-01	8.34e-01	9.92e-01
GO:0016482	68	1	0	1	9.88e-01	1.00e+00	9.27e-01
GO:0006793	279	9	4	5	9.94e-01	9.32e-01	9.82e-01
GO:0006796	272	8	3	5	9.97e-01	9.73e-01	9.79e-01
GO:0042000	15	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0044417	15	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0044766	15	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0051808	15	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0051836	15	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:1902579	15	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0002682	11	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0050776	11	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0051235	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0016197	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0042147	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0015858	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:1901264	6	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0051051	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006865	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006754	14	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006818	27	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009123	28	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009124	20	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009126	26	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009127	18	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009156	19	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009161	27	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009167	26	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009168	18	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0015985	14	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0015986	14	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0015988	14	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0015991	14	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0015992	27	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0046034	21	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0098655	25	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0098660	25	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0098662	25	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:1902600	23	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0070838	8	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0072511	8	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006152	21	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006184	19	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006195	21	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006913	26	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0007264	29	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009143	20	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009146	19	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009154	21	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009164	21	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009166	22	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009203	19	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009207	19	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009261	21	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0019439	42	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0034655	39	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0035556	44	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0042454	21	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0044270	44	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0046130	21	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0046434	25	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0046700	44	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0051169	26	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0072523	22	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:1901069	19	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:1901136	26	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:1901292	23	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:1901361	44	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:1901565	37	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:1901658	21	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0000278	17	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0000280	17	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0007067	14	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0022402	26	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0048285	18	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:1903047	16	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006302	6	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006473	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006432	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0030258	6	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006323	11	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006333	12	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006334	6	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0031497	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0034728	6	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0065004	11	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0071103	23	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0071824	11	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006352	15	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006367	8	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006721	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0016114	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0042273	16	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006612	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0045047	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0070972	9	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0072599	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0008643	6	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0008645	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0015749	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006733	18	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006743	8	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006744	8	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0042180	9	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0042181	9	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:1901661	9	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:1901663	9	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0035890	15	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0035891	14	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009072	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009073	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006383	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0097428	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0002376	12	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0002377	8	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0002440	8	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0042274	9	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0030154	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0048856	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0048869	8	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006631	37	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006633	23	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0072330	26	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0022411	9	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0032984	9	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0071826	32	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006836	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0043952	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0001522	17	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006415	6	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0043241	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0043624	6	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006855	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0015893	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006888	20	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0044053	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0015908	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006261	31	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0000387	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0022618	30	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006611	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0051168	8	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0000226	8	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0007020	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0031109	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0046785	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0051258	10	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006891	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006979	13	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006072	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0022900	12	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0022904	9	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0052646	6	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0071897	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0000393	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0016567	11	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006470	16	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0016311	20	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0050793	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009066	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009067	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0043604	6	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006486	13	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009100	13	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009101	13	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0043413	13	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0070085	14	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0010498	25	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0010564	18	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0030433	22	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0043161	25	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0010256	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006379	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006512	8	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006487	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0000245	9	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006270	12	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009063	8	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0016054	9	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0044282	9	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0046395	9	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:1901606	8	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006885	8	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0007035	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0030004	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0030641	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0045851	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0051452	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0051453	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0055067	8	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006749	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006750	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0019184	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0043043	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0044272	17	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009233	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009234	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006595	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
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GO:0008216	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0008295	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009309	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0042401	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0000041	9	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006826	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0015684	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006890	6	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0032269	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0051248	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006544	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009069	10	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009070	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009219	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009394	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0019692	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006410	6	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006405	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006606	10	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0034504	10	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0044744	10	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0051170	10	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:1902593	10	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0007186	6	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006429	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0030048	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006298	9	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006357	11	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006360	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006265	6	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0019751	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0034637	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0044262	11	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0001932	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009893	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0010604	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0031325	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0031399	6	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0032270	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0042325	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0043085	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0043549	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0044093	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0045859	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0048518	13	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0048522	10	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0051247	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0051338	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0000910	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006007	9	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006098	9	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006739	9	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006740	9	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006766	11	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006767	11	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0008614	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009110	10	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0019320	9	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0019362	10	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0042364	10	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0042816	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0042819	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0046365	9	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0046496	10	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0072524	13	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0072525	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0043484	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0008064	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0010639	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0030832	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0030833	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0030837	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0031333	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0032271	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0032272	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0032535	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0032956	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0032970	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0043244	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0043254	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0044087	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0051129	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0051493	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0051494	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0090066	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0000079	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0071900	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006772	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009228	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0042723	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0042724	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0015693	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0034982	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006607	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006643	21	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006664	18	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009247	17	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0046467	18	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0007167	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0007169	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006505	15	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006506	14	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006661	15	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0010638	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0030838	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0031334	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0032273	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0045010	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0051130	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0051495	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006401	10	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0018342	6	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0018344	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0097354	6	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0017004	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0000350	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0032784	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0034227	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006284	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0000302	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0000304	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0010035	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:1901700	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0030150	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009432	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009991	8	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0031668	6	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0071496	6	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0007033	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0007034	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006119	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006122	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0042773	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0042775	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0051260	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0043094	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0000096	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0032392	8	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0032508	8	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0015936	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0015937	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0033865	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0033866	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0033875	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0034030	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0034032	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0034033	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006370	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0008283	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006825	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0008535	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0046916	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0055076	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0030261	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006118	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006446	10	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0070925	15	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006434	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0030522	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0000956	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006402	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0040029	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006613	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006614	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0000027	8	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0042255	11	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009187	6	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009190	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0046068	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0052652	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0000724	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0000725	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006475	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0016573	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0018205	7	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0018393	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0018394	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009225	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0019673	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006084	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006085	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006086	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0035384	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0071616	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0000003	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0000394	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006388	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006787	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0033015	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0051187	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0016458	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006308	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006269	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0030488	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006420	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006541	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009084	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009200	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0045185	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0015074	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0000723	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0032200	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0060249	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0017182	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0017183	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0018202	6	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006665	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006166	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0043101	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0043174	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006914	6	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0032507	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0051651	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0031667	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0042594	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006471	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006040	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:1901071	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0000288	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0000290	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0046777	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006271	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0022616	5	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0016255	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0000070	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0000819	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0042777	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0022603	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006268	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006376	3	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006546	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0009071	4	0	0	0	1.00e+00	1.00e+00	1.00e+00
GO:0006424	3	0	0	0	1.00e+00	1.00e+00	1.00e+00

keg.test <- as.data.frame(do.call("rbind", lapply(kegg.gene.sets, function(gset) {
    set.size <- length(gset)
    gin_all <- gset[gset %in% top_genes_set$GeneID]
    gin_up <- gset[gset %in% top_genes_set$GeneID[top_genes_set$logFC > 0]]
    gin_down <- gset[gset %in% top_genes_set$GeneID[top_genes_set$logFC < 0]]
    result <- c(set.size = set.size, n.both = length(gin_all), n.up = length(gin_up), n.down = length(gin_down), p.value.both = phyper(length(gin_all) - 
        1, m = length(gset), n = total.genes - length(gset), k = nrow(top_genes_set), lower.tail = FALSE), p.value.up = phyper(length(gin_up) - 1, m = length(gset), 
        n = total.genes - length(gset), k = sum(top_genes_set$logFC > 0), lower.tail = FALSE), p.value.down = phyper(length(gin_down) - 1, m = length(gset), 
        n = total.genes - length(gset), k = sum(top_genes_set$logFC < 0), lower.tail = FALSE))
    return(result)
})))
keg.test <- keg.test[order(keg.test$p.value.both), ]
keg.test$Pathway <- kegg.annot.data$Pathway[match(rownames(keg.test), kegg.annot.data$`Pathway Id`)]
kable(keg.test, digits = 4)

	set.size	n.both	n.up	n.down	p.value.both	p.value.up	p.value.down	Pathway
ec00300	24	4	1	3	0.0606	0.4631	0.0590	Lysine biosynthesis
ec01053	24	4	1	3	0.0606	0.4631	0.0590	Biosynthesis of siderophore group nonribosomal peptides
ec00380	72	8	3	5	0.0817	0.2787	0.1321	Tryptophan metabolism
ec00053	8	2	1	1	0.0862	0.1870	0.2636	Ascorbate and aldarate metabolism
ec00790	10	2	0	2	0.1275	1.0000	0.0517	Folate biosynthesis
ec00565	32	4	4	0	0.1394	0.0084	1.0000	Ether lipid metabolism
ec00020	22	3	2	1	0.1580	0.1073	0.5693	Citrate cycle (TCA cycle)
ec00130	46	5	2	3	0.1614	0.3291	0.2476	Ubiquinone and other terpenoid-quinone biosynthesis
ec00140	3	1	0	1	0.1774	1.0000	0.1084	Steroid hormone biosynthesis
ec00660	3	1	1	0	0.1774	0.0747	1.0000	C5-Branched dibasic acid metabolism
ec00966	3	1	0	1	0.1774	1.0000	0.1084	Glucosinolate biosynthesis
ec00982	3	1	0	1	0.1774	1.0000	0.1084	Drug metabolism - cytochrome P450
ec00250	13	2	0	2	0.1958	1.0000	0.0832	Alanine, aspartate and glutamate metabolism
ec00710	13	2	0	2	0.1958	1.0000	0.0832	Carbon fixation in photosynthetic organisms
ec00440	4	1	0	1	0.2293	1.0000	0.1418	Phosphonate and phosphinate metabolism
ec00625	4	1	0	1	0.2293	1.0000	0.1418	Chloroalkane and chloroalkene degradation
ec00340	53	5	3	2	0.2401	0.1525	0.5970	Histidine metabolism
ec00010	27	3	0	3	0.2403	1.0000	0.0786	Glycolysis / Gluconeogenesis
ec00624	41	4	2	2	0.2571	0.2816	0.4586	Polycyclic aromatic hydrocarbon degradation
ec00941	41	4	2	2	0.2571	0.2816	0.4586	Flavonoid biosynthesis
ec00945	41	4	2	2	0.2571	0.2816	0.4586	Stilbenoid, diarylheptanoid and gingerol biosynthesis
ec00940	55	5	3	2	0.2643	0.1648	0.6173	Phenylpropanoid biosynthesis
ec00904	16	2	1	1	0.2673	0.3392	0.4579	Diterpenoid biosynthesis
ec00622	5	1	0	1	0.2779	1.0000	0.1740	Xylene degradation
ec00830	5	1	0	1	0.2779	1.0000	0.1740	Retinol metabolism
ec00970	43	4	1	3	0.2857	0.6725	0.2175	Aminoacyl-tRNA biosynthesis
ec00360	57	5	3	2	0.2890	0.1775	0.6368	Phenylalanine metabolism
ec00950	58	5	3	2	0.3015	0.1839	0.6463	Isoquinoline alkaloid biosynthesis
ec00253	59	5	3	2	0.3142	0.1904	0.6556	Tetracycline biosynthesis
ec00450	45	4	2	2	0.3146	0.3196	0.5078	Selenocompound metabolism
ec00626	18	2	1	1	0.3151	0.3726	0.4979	Naphthalene degradation
ec00640	19	2	1	1	0.3388	0.3887	0.5168	Propanoate metabolism
ec01057	48	4	2	2	0.3585	0.3479	0.5427	Biosynthesis of type II polyketide products
ec00600	20	2	2	0	0.3622	0.0912	1.0000	Sphingolipid metabolism
ec00906	20	2	1	1	0.3622	0.4043	0.5350	Carotenoid biosynthesis
ec00590	7	1	0	1	0.3662	1.0000	0.2349	Arachidonic acid metabolism
ec00591	7	1	0	1	0.3662	1.0000	0.2349	Linoleic acid metabolism
ec00720	21	2	2	0	0.3854	0.0991	1.0000	Carbon fixation pathways in prokaryotes
ec00361	8	1	0	1	0.4062	1.0000	0.2636	Chlorocyclohexane and chlorobenzene degradation
ec00363	8	1	0	1	0.4062	1.0000	0.2636	Bisphenol degradation
ec00910	8	1	0	1	0.4062	1.0000	0.2636	Nitrogen metabolism
ec00903	22	2	1	1	0.4081	0.4345	0.5693	Limonene and pinene degradation
ec00623	23	2	1	1	0.4304	0.4490	0.5856	Toluene degradation
ec00270	53	4	2	2	0.4313	0.3940	0.5970	Cysteine and methionine metabolism
ec00900	38	3	2	1	0.4326	0.2530	0.7671	Terpenoid backbone biosynthesis
ec00627	69	5	3	2	0.4415	0.2578	0.7379	Aminobenzoate degradation
ec00740	9	1	1	0	0.4436	0.2078	1.0000	Riboflavin metabolism
ec00942	55	4	3	1	0.4598	0.1648	0.8791	Anthocyanin biosynthesis
ec00522	40	3	2	1	0.4663	0.2721	0.7844	Biosynthesis of 12-, 14- and 16-membered macrolides
ec00051	25	2	1	1	0.4737	0.4768	0.6162	Fructose and mannose metabolism
ec00981	41	3	2	1	0.4829	0.2816	0.7925	Insect hormone biosynthesis
ec01051	41	3	2	1	0.4829	0.2816	0.7925	Biosynthesis of ansamycins
ec00362	26	2	1	1	0.4945	0.4903	0.6306	Benzoate degradation
ec00620	26	2	1	1	0.4945	0.4903	0.6306	Pyruvate metabolism
ec00350	58	4	3	1	0.5017	0.1839	0.8923	Tyrosine metabolism
ec00860	58	4	3	1	0.5017	0.1839	0.8923	Porphyrin and chlorophyll metabolism
ec00280	11	1	0	1	0.5117	1.0000	0.3435	Valine, leucine and isoleucine degradation
ec00650	27	2	2	0	0.5149	0.1504	1.0000	Butanoate metabolism
ec00480	29	2	1	1	0.5539	0.5285	0.6708	Glutathione metabolism
ec00680	29	2	1	1	0.5539	0.5285	0.6708	Methane metabolism
ec00760	13	1	1	0	0.5714	0.2858	1.0000	Nicotinate and nicotinamide metabolism
ec00030	14	1	0	1	0.5985	1.0000	0.4148	Pentose phosphate pathway
ec00920	14	1	1	0	0.5985	0.3040	1.0000	Sulfur metabolism
ec00310	49	3	1	2	0.6050	0.7199	0.5539	Lysine degradation
ec00330	33	2	1	1	0.6251	0.5751	0.7177	Arginine and proline metabolism
ec00260	17	1	0	1	0.6699	1.0000	0.4783	Glycine, serine and threonine metabolism
ec00642	17	1	1	0	0.6699	0.3561	1.0000	Ethylbenzene degradation
ec00730	17	1	1	0	0.6699	0.3561	1.0000	Thiamine metabolism
ec00983	17	1	0	1	0.6699	1.0000	0.4783	Drug metabolism - other enzymes
ec00604	18	1	1	0	0.6908	0.3726	1.0000	Glycosphingolipid biosynthesis - ganglio series
ec00965	18	1	1	0	0.6908	0.3726	1.0000	Betalain biosynthesis
ec00561	19	1	1	0	0.7103	0.3887	1.0000	Glycerolipid metabolism
ec01056	19	1	1	0	0.7103	0.3887	1.0000	Biosynthesis of type II polyketide backbone
ec00190	40	2	1	1	0.7281	0.6458	0.7844	Oxidative phosphorylation
ec00230	96	5	3	2	0.7327	0.4459	0.8813	Purine metabolism
ec00540	21	1	1	0	0.7458	0.4196	1.0000	Lipopolysaccharide biosynthesis
ec00564	62	3	2	1	0.7591	0.4729	0.9077	Glycerophospholipid metabolism
ec00562	22	1	0	1	0.7619	1.0000	0.5693	Inositol phosphate metabolism
ec00960	22	1	1	0	0.7619	0.4345	1.0000	Tropane, piperidine and pyridine alkaloid biosynthesis
ec00240	86	4	2	2	0.8004	0.6503	0.8396	Pyrimidine metabolism
ec00061	30	1	1	0	0.8589	0.5406	1.0000	Fatty acid biosynthesis
ec00040	6	0	0	0	1.0000	1.0000	1.0000	Pentose and glucuronate interconversions
ec00052	8	0	0	0	1.0000	1.0000	1.0000	Galactose metabolism
ec00062	7	0	0	0	1.0000	1.0000	1.0000	Fatty acid elongation
ec00071	21	0	0	0	1.0000	1.0000	1.0000	Fatty acid degradation
ec00195	22	0	0	0	1.0000	1.0000	1.0000	Photosynthesis
ec00231	13	0	0	0	1.0000	1.0000	1.0000	Puromycin biosynthesis
ec00281	5	0	0	0	1.0000	1.0000	1.0000	Geraniol degradation
ec00351	3	0	0	0	1.0000	1.0000	1.0000	DDT degradation
ec00364	7	0	0	0	1.0000	1.0000	1.0000	Fluorobenzoate degradation
ec00400	9	0	0	0	1.0000	1.0000	1.0000	Phenylalanine, tyrosine and tryptophan biosynthesis
ec00410	5	0	0	0	1.0000	1.0000	1.0000	beta-Alanine metabolism
ec00500	5	0	0	0	1.0000	1.0000	1.0000	Starch and sucrose metabolism
ec00510	9	0	0	0	1.0000	1.0000	1.0000	N-Glycan biosynthesis
ec00512	3	0	0	0	1.0000	1.0000	1.0000	Mucin type O-Glycan biosynthesis
ec00513	10	0	0	0	1.0000	1.0000	1.0000	Various types of N-glycan biosynthesis
ec00520	23	0	0	0	1.0000	1.0000	1.0000	Amino sugar and nucleotide sugar metabolism
ec00521	5	0	0	0	1.0000	1.0000	1.0000	Streptomycin biosynthesis
ec00550	11	0	0	0	1.0000	1.0000	1.0000	Peptidoglycan biosynthesis
ec00563	22	0	0	0	1.0000	1.0000	1.0000	Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
ec00592	12	0	0	0	1.0000	1.0000	1.0000	alpha-Linolenic acid metabolism
ec00601	3	0	0	0	1.0000	1.0000	1.0000	Glycosphingolipid biosynthesis - lacto and neolacto series
ec00603	3	0	0	0	1.0000	1.0000	1.0000	Glycosphingolipid biosynthesis - globo series
ec00630	11	0	0	0	1.0000	1.0000	1.0000	Glyoxylate and dicarboxylate metabolism
ec00633	4	0	0	0	1.0000	1.0000	1.0000	Nitrotoluene degradation
ec00670	9	0	0	0	1.0000	1.0000	1.0000	One carbon pool by folate
ec00750	3	0	0	0	1.0000	1.0000	1.0000	Vitamin B6 metabolism
ec00770	9	0	0	0	1.0000	1.0000	1.0000	Pantothenate and CoA biosynthesis
ec00780	16	0	0	0	1.0000	1.0000	1.0000	Biotin metabolism
ec00785	4	0	0	0	1.0000	1.0000	1.0000	Lipoic acid metabolism
ec00908	4	0	0	0	1.0000	1.0000	1.0000	Zeatin biosynthesis
ec00930	8	0	0	0	1.0000	1.0000	1.0000	Caprolactam degradation
ec00944	3	0	0	0	1.0000	1.0000	1.0000	Flavone and flavonol biosynthesis
ec01040	6	0	0	0	1.0000	1.0000	1.0000	Biosynthesis of unsaturated fatty acids

Gene sets from Daily et al and Shock et al

We now test using roast and camera for deregulation of gene sets obtained from the papers:

Daily, J. P., D. Scanfeld, N. Pochet, K. Le Roch, D. Plouffe, M. Kamal, O. Sarr, et al. 2007. “Distinct Physiological States of Plasmodium Falciparum in Malaria-Infected Patients.” Nature 450 (7172): 1091–95.

Shock, Jennifer L., Kael F. Fischer, and Joseph L. DeRisi. 2007. “Whole-Genome Analysis of mRNA Decay in Plasmodium Falciparum Reveals a Global Lengthening of mRNA Half-Life during the Intra-Erythrocytic Development Cycle.” Genome Biology 8 (7): R134.

setwd(wd)

# Load gene lists from Daily et al and Shock et al
daily_figure2 <- fread("./data/daily_expression_figure2.csv", data.table = FALSE, header = TRUE)

JLshock <- c("PF3D7_0320800", "PF3D7_0410400", "PF3D7_0507600", "PF3D7_0520300", "PF3D7_0720000", "PF3D7_0811300", "PF3D7_0819900", "PF3D7_0909400", "PF3D7_0909900", 
    "PF3D7_1006100", "PF3D7_1032100", "PF3D7_1103800", "PF3D7_1106300", "PF3D7_1107000", "PF3D7_1124400", "PF3D7_1128600", "PF3D7_1209200", "PF3D7_1224300", 
    "PF3D7_1235300", "PF3D7_1307000", "PF3D7_1308900", "PF3D7_1325000", "PF3D7_1340100", "PF3D7_1364500", "PF3D7_1427800", "PF3D7_1443300", "PF3D7_1443500", 
    "PF3D7_1449700", "PF3D7_0519500")

# Load entrex geneID mappings
entrez_geneID_mappings <- fread("./data/geneID_mappings.txt", data.table = FALSE, stringsAsFactors = FALSE)

upcluster2 <- daily_figure2$Gene[daily_figure2$`Up regulated in Cluster 2?` == "Y"]
upcluster1 <- daily_figure2$Gene[daily_figure2$`Up regulated in Cluster 2?` == "N"]
glycolisis <- daily_figure2$Gene[daily_figure2$type == "Glycolisis"]
tricarboxylic <- daily_figure2$Gene[daily_figure2$type == "Tricarboxylic acid cycle"]
fatty_acid <- daily_figure2$Gene[daily_figure2$type == "Fatty acid metabolism"]

upcluster2 <- as.vector(geneID_mappings$current[geneID_mappings$old %in% upcluster2])
upcluster1 <- as.vector(geneID_mappings$current[geneID_mappings$old %in% upcluster1])
glycolisis <- as.vector(geneID_mappings$current[geneID_mappings$old %in% glycolisis])
tricarboxylic <- as.vector(geneID_mappings$current[geneID_mappings$old %in% tricarboxylic])
fatty_acid <- as.vector(geneID_mappings$current[geneID_mappings$old %in% fatty_acid])

indices <- ids2indices(list(up_in_starvation = upcluster1, up_int_vitro = upcluster2, glycolisis = glycolisis, tricarboxylic = tricarboxylic, fatty_acid = fatty_acid, 
    mRNA_degradation = JLshock), rownames(v2$E))
mroast(v2, index = indices, design = modRUV, contrast = 2, nrot = 10000, set.statistic = "floormean")

##                  NGenes  PropDown     PropUp Direction     PValue        FDR PValue.Mixed  FDR.Mixed
## up_int_vitro         12 0.8333333 0.00000000      Down 0.01189881 0.02647235   0.01259874 0.01877812
## mRNA_degradation     29 0.2758621 0.06896552      Down 0.01629837 0.02647235   0.00869913 0.01877812
## glycolisis           19 0.5789474 0.05263158      Down 0.01699830 0.02647235   0.01569843 0.01877812
## tricarboxylic        11 0.1818182 0.36363636        Up 0.01769823 0.02647235   0.00119988 0.00689931
## up_in_starvation     33 0.1818182 0.21212121        Up 0.06339366 0.07601240   0.01179882 0.01877812
## fatty_acid           17 0.1764706 0.11764706        Up 0.12238776 0.12238776   0.07189281 0.07189281

camera(v2, index = indices, design = modRUV, contrast = 2)

##                  NGenes Direction       PValue          FDR
## up_int_vitro         12      Down 1.470968e-05 8.825807e-05
## glycolisis           19      Down 1.322405e-03 3.967216e-03
## mRNA_degradation     29      Down 8.826335e-02 1.765267e-01
## up_in_starvation     33        Up 2.390539e-01 3.166989e-01
## tricarboxylic        11        Up 2.639157e-01 3.166989e-01
## fatty_acid           17        Up 3.466823e-01 3.466823e-01

Summary Gene Set Plot

summary.set.data <- fread("./data/genes_in_set_for_figure2.csv", data.table = FALSE)
gg <- ggplot(summary.set.data, aes(x = Gene, y = `adj-p`, fill = logFC))
gg <- gg + geom_col() + coord_flip() + facet_wrap(~SetName, scales = "free_y")
gg <- gg + scale_fill_gradient2(low = "#0571b0", high = "#ca0020", mid = "#ffffff")
gg <- gg + scale_y_continuous(limits = c(0, 0.15))
gg <- gg + theme_bw(base_size = 8)
gg

System Information

setwd(wd)
sessionInfo()

## R version 3.4.3 (2017-11-30)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: OS X El Capitan 10.11.6
## 
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
## 
## attached base packages:
##  [1] grid      stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] pheatmap_1.0.8             knitr_1.17                 stringr_1.2.0              dplyr_0.7.4                data.table_1.10.4-3       
##  [6] VennDiagram_1.6.18         futile.logger_1.4.3        RColorBrewer_1.1-2         EDASeq_2.10.0              ShortRead_1.34.2          
## [11] GenomicAlignments_1.12.2   SummarizedExperiment_1.6.5 DelayedArray_0.2.7         matrixStats_0.52.2         Rsamtools_1.28.0          
## [16] GenomicRanges_1.28.6       GenomeInfoDb_1.12.3        Biostrings_2.44.2          XVector_0.16.0             IRanges_2.10.5            
## [21] S4Vectors_0.14.7           BiocParallel_1.10.1        Biobase_2.36.2             BiocGenerics_0.22.1        reshape2_1.4.3            
## [26] ggplot2_2.2.1              ruv_0.9.6                  quadprog_1.5-5             edgeR_3.18.1               limma_3.32.10             
## 
## loaded via a namespace (and not attached):
##  [1] bit64_0.9-7             splines_3.4.3           R.utils_2.6.0           assertthat_0.2.0        statmod_1.4.30          highr_0.6              
##  [7] aroma.light_3.6.0       latticeExtra_0.6-28     blob_1.1.0              GenomeInfoDbData_0.99.0 yaml_2.1.16             RSQLite_2.0            
## [13] backports_1.1.2         lattice_0.20-35         glue_1.2.0              digest_0.6.13           colorspace_1.3-2        htmltools_0.3.6        
## [19] Matrix_1.2-12           R.oo_1.21.0             plyr_1.8.4              pkgconfig_2.0.1         XML_3.98-1.9            biomaRt_2.32.1         
## [25] genefilter_1.58.1       zlibbioc_1.22.0         xtable_1.8-2            scales_0.5.0            tibble_1.3.4            annotate_1.54.0        
## [31] GenomicFeatures_1.28.5  lazyeval_0.2.1          survival_2.41-3         magrittr_1.5            memoise_1.1.0           evaluate_0.10.1        
## [37] R.methodsS3_1.7.1       hwriter_1.3.2           tools_3.4.3             formatR_1.5             munsell_0.4.3           locfit_1.5-9.1         
## [43] bindrcpp_0.2            lambda.r_1.2            AnnotationDbi_1.38.2    compiler_3.4.3          DESeq_1.28.0            rlang_0.1.6            
## [49] RCurl_1.95-4.8          labeling_0.3            bitops_1.0-6            rmarkdown_1.8           gtable_0.2.0            DBI_0.7                
## [55] R6_2.2.2                rtracklayer_1.36.6      bit_1.1-12              bindr_0.1               rprojroot_1.3-1         futile.options_1.0.0   
## [61] stringi_1.1.6           Rcpp_0.12.14            geneplotter_1.54.0